It makes perfect sense, actually. ROM hacks are running native code, made exclusively for the 3DS. Emulators have to pretend to be an entire machine, including the processor, graphics, sound, input, etc. Emulation has a lot more overhead than simply running a 3DS game on a 3DS.
Emulation takes a while to perfect, especially on weaker hardware. Homebrew for the 3DS didn't really take off until this past year or so. So just give it time (and effort if you're willing to test or develop).
Project 64 has a lot of issues tbh. Especially graphical glitches. For example when I played smash 64 on a fresh download of project 64 it was basically impossible to see any items.