Is there a baseq2/qconsole.log or something like that in the nxquake2 folder?
There should be at least 3 files in the nxquake2 folder: ref_gl3.so, ref_soft.so and nxquake2.nro. Verify that all of them are present and not corrupted or something.
My man fgsfds you are just the great hero of the Switch homebrew gaming scene!.. Morrowind, GZdoom, Xash3D, Quake 1/2 and much more other excellent ports.