I am sure that they are also conscious of the changes happening in their voices. It maybe that due to that they are not participating in the fear of being made fun of.Before it used to be about just knowing the song but now its also about singing it with tune .
I don't think singing has anything to do with girls or is something more to the inclination for girls since in most talent shows we also get to see good talented boys and a lot of them later on go to become popstars and band members.Its not the singing that they are interested in but the kind of music. Those who do choose singing are more inclined to classical singing and since antakshri is about your display of filmy knowledge they lack out.
Instead of taking up singing lots of boys prefer to learn instruments like guitar or the tabla . Their focus is on classical music and raaga's that then later get developed to filmy music . Most of these people are again not exposed as filmy music that goes against them in giving a shot on antakshri.
Lastly also parents encouragement is a huge factor. Most parents don't really seem to encourage their sons in music and prefer to have them excel is sports or studies. If they were to tell them they want to be a singer I am sure it does not digest down well. After all still in the indian society the male is the head of household shouldering the responsibilities.
One thing that would be interesting to know is the real count on the boys participation. Is it due to lack of participation on the boys side that we do not see them or is it due to the lack of knowledge that we do not see them???