I really don't think these are anti-emulation measures. The Classic NES Series games weren't ports of NES games, they were NES emulators packaged up with the NE

I really don't think these are anti-emulation measures. The Classic NES Series games weren't ports of NES games, they were NES emulators packaged up with the NES ROMs running on the GBA. The "measures" detailed on that article sound more like either bugs in the GBA emulator, or tricks that Nintendo used to squeeze the most speed out of their own NES emulator.