While I fully respect your right to code it as you see fit, I foresee the filename limit being a hindrance to some. Just looking through the list of NES roms on my computer, I can see at least a dozen or so games that will need to be renamed in order to work with your emulator. These days, people are more likely to simply download the entire collection and copy it over without looking at the individual files first. The other likely scenario is that they're simply copying their pre-existing collection for use with 3DNES.
Unless the filename limit is something that is necessary for performance reasons, I don't see a need to have one in the first place. Considering that the roms are stored on the 3DS SD card, there are more steps required to fix a rom's name than if the roms were stored on the microSD, especially on 3DSes with an emuNAND setup. From a standpoint of user-friendliness, a fewer amount of times you need to use your PC for setup leads to higher user retention. While this isn't much an issue while the homebrew scene is in its infancy, this won't always be the case. Eventually the scene will mature and there will likely be more than one emulator for a given system. Don't let the current lack of competition foster complacency.
Right now, your emulator is the standard-bearer for NES emulation on the 3DS, whether or not you realize it. Why not use that position to establish a standard of excellence? I appreciate all of the contributions you have made so far to make NES emulation possible. I just wanted to point out some of the overlooked consequences of current limitation. I know that this project is only going to get better with time.