If you look at past consoles with CFW, generally online will work, but with the caveat that you risk getting banned. If online becomes particularly popular for certain games, I wouldn't be surprised to see most people with modded consoles to pick up a second non-modded one. That's probably the route I'll go.
Judging by Nintendo's current attitude towards keeping the modding scene under control, I'd be willing to bet that they'll attempt to keep modded consoles from properly accessing the online service without a ban.