The DaedalusX64 PSVita compatibility list states that this is a known issue with Starcraft 64. The 2DS/3DS compatibility list shows Starcraft as untested, but presumably it is the same issue as with the Vita version of the emulator.
In reply to: starcraft64
posted by deadmanaof
Does anyone know why starcraft64 crashes. I've downloaded it to my emulator on my 2ds and psvita and neither can boot the game without crashing