Just like all of us, the characters in the comic are entitled to their own opinions about V's gender, although those opinions are not necessarily correct. The Giant actually answers this question in the FAQ:
http://www.giantitp.com/FAQ.html#faq10Q: Is Vaarsuvius male or female?
A: I will never reveal the truth! Bwahaha! Keep in mind that while certain other characters might refer to V as being male or female, that simply reveals their perception.not the actual reality of the situation.