If you use a Gateway, then no it won't matter at all.
You can rename the .3ds files to whatever you like (excl. fancy special characters of course). The saves are usually stored on your SD card (the one inside the 3DS) and are using the game's real title ID (check them here:
http://3ds.essh.co/) and a .sav extension for naming. If you rename a rom then the gateway will still load up the correct savegame. There are some games like Pokémon X/Y/OR/AS, Animal Crossing New Leaf and a few others that don't store the savegame on the SD card but inside the rom itself, so it also doesn't matter if you rename them, saves will still work
