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In theory it's possible if you keep in all the original scripts. I was able to successfully have a multiplayer mode, but it was Battles Only.
You might have problems if you try to trade between two different games because if you changed certain things too much, you might get glitchy results on one or both ends. Which could potentially be interesting, but that prospect probably keeps people from bothering to keep the trading feature in a lot of the time.
You could probably trade between two of the same version of a hack assuming the scripts weren't overwritten or bugged. If you mean transferring to an actual Pokemon game, it may be possible if there aren't expanded Pokemon but again it depends on factors including the ones I previously mentioned.
For trading from an emulator you need to set up a network.. But that's out of my knowledge. But if you have a console with you then you might wanna try a R4 Card. They are cheap and you can easily play any rom hacks on them. As long as it is without any major bugs of course.
There you are also able to trade, battle and connect between different rom hacks and also even the original games. The thing is like AkameTheBulbasaur and amitydev already stated correctly, if you wanna trade Fakemon or Pokémon that are not in the game you want to connect with (also with battle) than the games will crash and there can be heavy damage to the console or the cartridge. Fixable but not quite fun xD
Being able to trade or link-battle across the web would be amazing. Hopefully that'll become a reality at some point. My only concern would be how you control trades/battles against hacked Pokemon if you want that vanilla experience.