Thanks for the interesting question:
Avos Derabbi Nosson 34:5 cites two possibilities, one is that this kiss was particularly sincere or non-sincere, and the other is that these are markers that denote a scribal addition made based on doubt:
וירץ עשו לקראתו ויחבקהו ויפול על צואריו וישקה״ו (שם לג) כולו נקוד מלמד שלא נשקו באמת. ר״ש בן אלעזר אומר נשיקה זו של אמת וכולן אינן של אמת.
למה אלא כך אמר עזרא אם יבא אליהו ויאמר לי מפני מה כתבת כך אומר אני לו כבר נקדתי עליהן ואם אומר לי יפה כתבת אעביר נקודה מעליהן.
1. Commentaries that support "scribal additions":
Some manuscripts of the Ibn Ezra's commentary contain the following addition, which sounds like he supports the view that Ezra added this word to the Torah, because he wasn't sure whether or not it originally belonged:
נקודות על וישקהו – [וכן י״ד אחרים בכל המקרא, והיודע סודם נפטר, כי היה שמו עזרא.]
Shadal notes that the verse would make perfect sense even if that word was not originally present (compare Bereishis 46:29, with Ya'akov and Yosef, where the text does not say explicitly that he kissed him, but also notes that many scholars support this view, and cites textual support from Origen. I don't have access to it (nor do I even know what remains of this part of the Torah), but the Septuagint here, Peshitta here, and Samaritan Torah here all have it in their texts. There are no Dead Sea scrolls that contain these verses. The Targumin seem to by and large follow the other interpretation, as we will mention.
As noted by the commentaries to Maseches Sofrim, this understanding is accepted by Tosfos (Piskei Tosfos Menachos 232) and the Taz (YD 274), and they Pasken that therefore, a Sefer Torah missing these dots is still Kosher.
2. Commentaries that support a Midrashic reading
Various other commentaries quote Midrashim that address this. The Midrash (Pirkei Derabbi Eliezer, cited in Minchat Shai here, but also in other Midrashim, and Sifsei Chachamim has another interesting version) tells us:
אל תקרי וישקהו אלא וישכהו
Don't read [this word as] "and he kissed him", rather [as] "and he bit him".
Rabbi Yanai in Bereishis Rabbah here makes the inference from the dots over this word, as opposed to directly from the possible swapped reading. No one says clearly that they are meant to be bite marks, though... :)
Many of the mefarshim (including Radak, Tur, Minchat Shai, Sifsei Chachamim, Targum Pseudo-Yonasan, Yerushalmi, and the Targum Neofiti marginal notes) follow this understanding of the Passuk.
Various other mefarshim (I'm not making another list) quote other Midrashim here that suggest what we saw in Avos Derabbi Nosson (also found in many other Midrashic sources, such as Bereishis Rabbah), that this is telling us about Esav's intentions, that it was not sincere, or that only this time it was sincere.
3. Alternative understandings
Ralbag notes that this was dotted to show that it was something between a kiss and a non kiss, and is thus suspended between being written and not being written (therefore it is dotted). (This sort of fits with approach #2, and a bit with approach #1.)
Rav Dovid Zvi Hoffman suggests that the dots were added to emphasize that this word remained in the text, because it would be easy to think that it was not true. Quite original.
To conclude - we cannot say definitively which of the above approaches is correct (although we can say that they were not intended as bite marks). If we follow the Piskei Tosfos and Taz, we can say that the Torah originally MAY have omitted this entire word, and Ezra filled it in due to doubt.