I'd be surprised if signature patches truly didn't apply to 3DS cartridges. While it might not be quite the same thing, they work for Gateway, which more or less behaves like a retail cartridge (ignoring the multi ROM stuff). The issue here is that the Sky 3DS itself refuses to mimic anything without valid signatures. Whether or not that's an artificial limitation, I don't know, although it has the benefit of letting the user know immediately that a given ROM is invalid (the Sky 3DS+ renames bad roms to *.3ds.bad, or something similar). With the rise of CFW, I think it would be to their advantage to make ROM hacks work, but it seems it's currently aimed towards those with completely non-hacked consoles.