As far as I know, the only commandments followed by Karaites are those that are in explicitly stated in the Torah. Why wear a yarmulke if this isn't commanded in the Torah? Here is a link about Karaite Synagogue Etiquette
Karaites despite their rejection of Rabbinic Judaism still have their own traditions on how certain laws are kept, they have their own sages, and their own culture etc. Their religion is not exclusively limited to a literal understanding of Torah with no other instructions.
They wear a kippah to synagogue only because it was traditionally Jewish elements of worship. Before kippahs, they wore a fez. Before a fez, it was a turban. But the bottom line was that head coverings were worn during prayer in their synagogues so they still are today.