Will emu4ios void my iPod Touch's warranty?

Whether it voids the warranty or not is a determination for Apple. However I'd say if the app is available in the App store then Apple is fine with it. If it's not, then I wouldn't use it.

Since it is bypassing the App Store in iTunes, I would be willing to bet if you took your iPod to Apple and they found Emu4ios on it they would just hand it back to you and say it is your problem.

Not only that, I just checked the Emu4ios website and the Emu4ios store is labeled under "not working".