How is it that many Teimanim wear long peyos (simanim) similar to many Chasidim, considering that their culture has been mostly isolated from Ashkenazi Europe? Do any historical sources tell us when and why their custom originated?
HaRav Yoseph Qafih zt"l writes in his book Halikhoth Teman that it was a custom primarily of kohanim who came to Yemen in antiquity.
And the idea that Yemenite Jewry was isolated from the Jewish world and its literature throughout the ages is a myth. Adan was a port city and other ports on the coast of Yemen were a frequent stop for those sailing around Africa. They had all types of sepharim from various Jewish communities world-wide, including the Hasidic communities of Europe, and those in Germany. Another similar myth, i.e. that the Qehiloth Teman followed the Rambam simply because they did not know about the Shulhan `Arukh, is also completely false and contradicts the wealth of historical sources and rabbinic correspondence and responsa - some dating back to the times of the Geonim - that indicate that the Yemenites were very aware of the Jewish world around them and in the greater Diaspora.
Their historical isolation was from the Muslim population within their own country and not from Judaism at large. So, in relation to your question: scholarly evidence points to peyoth (or simanim, as they are referred to in the Yemenite community) being a continuation of ancient custom hinted at in other ancient archaeology of Egypt and the Levant. In fact, Yehezqel HaNavi (also a kohen) refers to being lifted by the "ssissith roshi" which seems to also infer to this practice being originally a midath hasiduth in the priestly families of old.
My own opinion as to the sources of these rumors and theories is that many in the Haredi community cannot fathom anyone choosing to follow the Rambam or other authorities after the publication of the Shulhan`Arukh and the popularization of the teachings of Yisshaq Luria. However, they chose him and follow him due to his greatness in halakhah and purity of reasoning.
I hope that this helps. Kol tuv.
tl;dr It may have possibly come from the prohibition of "nor shall you follow their laws" (בחוקותיהם לא תלכו), as there are testimonies that the ancient Arab tribes would shave and clip their peyot.
Chaggai Mazuz in his essay in Hebrew "The tradition of growing peyot among the Jews of the northern Arabian Peninsula" discusses the subject of both the origins of the minhag of the Teimani Jews and the possibility that also the Arabian Jews kept this minhag. In it he writes:
"Immediately after Qifakh [Rabbi Kapach] wrote that the growing of peyot was kept already at the time of the First Temple and that the Jews of Teiman kept this minhag in the lands of the gentiles, he added: "We have a tradition among us that our forefathers came to Teiman at the end of the First Temple era when they heard the prophecy of Yirmiyahu about the coming destruction, and they stood and went into exile of their own free will, at first to a nearby area, and later before Teiman."...likely he meant that "a nearby area" was the northern part of the Arabian Peninsula...
...reinforcing the idea that the Jews were exiled to Khijaz due to the exile of Ashur in the 8th century BCE we can find in the prophecy of Yesha'yahu...he mentioned Dedan and Teiman in the northern Arabian Peninsula: "The Arabia Pronouncement. In the scrub, in Arabia, you will lodge, O caravans of the Dedanites! Meet the thirsty with water, You who dwell in the land of Tema; Greet the fugitive with bread. For they have fled before swords: Before the whetted sword, Before the bow that was drawn, Before the stress of war." (Yesha'ayahu 21:13-15). Dedan can be found at a distance of three days' riding from the Jewish settlement Khaibar and around six days' riding from Almedina...it seems therefore that among the Teimani scholars there was a disagreement about what era Jews first came to Teiman...but everyone agreed that on the way they passed through Khijaz...
In order to prevent assimilation with the neighboring nations and the adoption of their paganist practices, the Torah prohibited Bnei Yisrael certain practices that can be seen as becoming similar to the non-Jews: "You shall not copy the practices of the land of Egypt where you dwelt, or of the land of Canaan to which I am taking you; nor shall you follow their laws." (Vayikra 18:3). The prohibition of shaving the peyot of the head (Vaykira 19:27) appears among a line of prohibitions of following the practices of the non-Jews, but the Torah didn't explain specifically the reason of the prohibition.
It's possibly that we may find a hint to the reason of this prohibition in an external source. According to the father of history, Herodotus (485-420 BCE), the Arabs would shave the peyot of their heads as an example of their pagan beliefs: "they say that the cutting of their hair is done after the same fashion as that of Dionysos himself; and they cut their hair in a circle round, shaving away the hair of the temples." (Histories Book III:8). Herodotus is referring to the confederation of Arabian tribes on the southern border of Eretz Yisrael.
From Tanach an image arises of a Jewish settlement in the southeast of Eretz Yisrael and in Ever Hayarden, a settlement that had close ties with the Arabian tribes. Yericho, Tzo'ar, Eilat and in their surrounding areas were the northern side of this settlement, and from there to the south there was a line of Jewish settlements. From the testimony of Herodotus we may understand the reason for the prohibition of Bnei Yisrael to shave the peyot of their head.
From Yirmiyahu it seems that this minhag of shaving the peyot wasn't just typical to the Arabs who lived on the southern border of Eretz Yisrael, but also the Arabian tribes who lived even further south, meaning, in the northern Arabian Peninsula..."of Egypt, Judah, Edom, the Ammonites, Moab, and all the desert dwellers who have the hair of their temples clipped." (Yirmiyahu 9:25), "Dedan, Tema, and Buz, and all those who have their hair clipped; all the kings of Arabia, and all the kings of the mixed peoples who live in the desert" (Yirmiyahu 25:23-24), "...And I will scatter to every quarter Those who have their hair clipped..." (Yirmiyahu 49:32). ...therefore "those who have their hairs clipped" settled southwest of the Kingdom of Edom, re: in the northern Arabian Peninsula...from the words of Herodotus and Yirmiyahu we see an image forming according to which the clipping of the peyot was popular among the Arabs from the southern border of Eretz Yisrael all the way to Khijaz. In this area lived Arab tribes and most of them were nomadic or partially nomadic. Qifakh wrote that already on the eve the destruction of the First Temple were exiled Jews with long peyot to the northern Arabian Peninsula, and that is the same area that Yirmiyahu mentioned...if we accept the traditions of the scholars of Teiman as reliable, we conclude that in 8th and 7th centuries BCE there were in the northern Arabian Peninsula two groups with opposite traditions: Jews who grew out their peyot, and Arabs who clipped them.
Lastly, about the Jews of Arabia specifically: Mazuz brings two non-Jewish sources that even back in the time of Muhammad, Jews, at least those in Arabia, grew out their peyot:
a. According to Islamic traditions, the Jews of Almedina lived by two Arab tribes, Awas and Khazraj. Zayid ben Thabit was originally an Arab, of the sons of Alnajar, one of the houses of Khazraj. According to Muslim sources he was a Jew with peyot who was educated by Jews, and since he was an Arab by birth, it is likely that he converted. However, some time after the rise of Islam, he converted to Islam...in the Hadith it is said that Abad Allah ben Mas'ud was asked if he reads the Quran like Zayid ben Thabit does, and replied: "What is it to me and Zayid and the way he reads? I heard from the messenger of Allah seventy surahs even when Zayid ben Thabit was a Jew with two peyot."
b. The Khanbalian jurist Ahmad ben Abad AlKhalim Taki Ibn Taymiah (1263-1328) wrote...in the book Ibn Taymiah attacked Jews, Christians, the Zoroastrians...according to a tradition brought in the book of Ibn Taymiah a short time after the death of Muhammad, his assitant Anas ben Malikh saw Alkhajaj ben Alkhassan, who was then a young man, who had on his head two peyot (qutzatan) and commanded him to shave them immediately for that is a tradition of the Jews. Per the tradition about Zayid ben Thabit and the one about Alkhajaj ben Alkhassan, we can assume that when Zayid...converted, he grew out his peyot, an tradition that differentiated between the Jewish settlers and their Arab neighbors in Almedina, and after he became a Muslim, he shaved off his peyot, to differ from the Jews.
It seems from the Tshuvos HaRambam 244 that one does not need to grow their payos long and in fact the Rambam did not grow his long.However in this tshuvah it seems the masses had such an idea of growing them long. http://www.hebrewbooks.org/pdfpager.aspx?req=1731&st=&pgnum=170
The Ben Ish Chai in his drashos on parshas zachor brings a proof from Mordichai that he had long payos see his Toras Lshima siman 389(If I rem correctly) which talks about growing long payos ss well.