No they aren't actually, when it comes to reading roms... I still wouldn't recommend a flash drive due to the finite read/write, but larger files will stutter when loading via a mechanical hdd compared to a flash drive, and depending on what format they're in, they might not even run at all: I couldn't even load half the rvz gamecube files I had when setting it up on my brothers Xbox using a mechanical (also lots of stutter ingame on ppsspp for example), yet as soon as I switched to a flash drive on the same system for him, no problems...
OP: stick with your flash drive if you don't fancy ftp and are playing anything from, ooh, Dreamcast upwards: the only upgrade I'd recommend is an external ssd (like I've got ...but they're expensive I know...)