That's odd, I always play with wifi on with 3DS since it is on a network like Live or PSN.This is where Friend List on handhelds are kind of useless -- thanks to weak battery tech. To save battery life no one will have wifi on unless the game needs it, so you'll never see many people online with Vita -- exactly like the 3DS.
I'll be doing the same with Vita.
Now that I think about it though, it is kind of useless on 3DS unless the game is 'online' since you can't send messages or do much with it.