That is not the case. Granted, I've only had mine since Monday and only a couple days "hacked", but every game has worked flawlessly thus far, and nothing leads me to believe it will change.
The ROM set that I have [Cylum's NES ROM set (highly recommend)] has each game as a .zip. The Hakchi program that I used to dump the original kernel / flash new kernel supports these .zip file types without issue. Likewise, with the games I've installed (original 30 + the additional), I'm only using 49MB out of the 300MB capacity available. In fact, the the entirety of the 700 game ROM set is only 67.5MB. I just didn't want Barbie, Fisher Price games, etc, amongst others that I left out.
Anyhow, performed the same routine on my coworkers and his is functioning properly as well. This includes save states, menu features, etc for the original games as well as the new ones.