Nothing will change in the save respect, whether you use EmuNAND or not, Romset and save compatability is the same, If you only play backups and dont care about eshop, playing retails etc, EmuNAND isnt needed, Since we are still booting into EmuNAND from 4.1-4.5 regardless of its version, at present it all uses the old KeyY method, if you only play roms, you wont loose saves and shouldn't regardless of emuNAND or systemNAND as they are all on your sd card anyway..
The loosing saves is for retail games that come with an update partition of 6.x and have been played on a legit 6.3 system, prior to playing them on Gateway, GW doesnt know the new crypto or flags so reinitializes the save or gives save corrupt message, If you havent played the retails on a 6.3 System they will play/save fine, Just at the moment they cant be Swapped, If you played on GW and saved, it wont play on a 6.3 System, and vice versa