The anti-piracy system is a continuation of the Super Nintendo's CIC model. As you know, earlier bootleg detection and region locking were enforced by the CIC chip (which was present in every authorised game cartridge) . The Nintendo 64 enhanced this system by assigning specific CIC chip variants to individual games, ensuring that each cartridge was not a counterfeit or contained a CIC clone.
To enforce this, the PIF-NUS conducts checksum verifications both at the startup and during gameplay to supervise the current CIC installed on the cartridge.
If the PIF determines the current cartridge is not valid, it forces the console into a permanent freeze state.
Moving on, region locking was done by slightly altering the shape of the cartridge on a region basis, so users could not physically insert the game into a console from a different region.
Overall, piracy wasn't a significant concern due to the inherent complexity and cost of replicating cartridges, though game prices were often three times higher than CD-based titles.
Unused ports
As silly as it may seem, Nintendo left one door open: The Disk Drive port.
The Doctor V64 attached to the console .
The back of the V64 , showing some interesting A/V.
A few companies reversed-engineered the interface to develop their own peripherals, and some of the resulting products became a concern for piracy.
I guess the most notable case was the Doctor v64, a device resembling the Disk Drive but equipped with a CD-ROM drive instead.
This expansion could back up the contents of the cartridge to a CD, the opposite (reading ROM files from a CD) was also supported.
Emulation
When I was a kid, I used to play some N64 games on a Pentium II machine using an emulator. It wasn't that bad, though in hindsight, I'm amazed my old computer managed to emulate a complex 64-bit machine - especially given that, among other things, my PC barely had enough RAM to keep the integrated video alive.
The truth is, while reproducing the architecture of this console can be complex, microcode routines will give a hint of what the console is trying to achieve, and since emulators don't have to be cycle-accurate, they can apply enough optimisations to provide extra performance in exchange for precision .
Another reason is the 64-bit instruction set: since games rarely took full advantage of them, emulation performance was hardly affected when running on a 32-bit host computer.