The N64 SDK (Libultra) was leaked a while ago and is all proprietary, owned by Nintendo. Portal 64 was issued a DMCA by Valve partly on account of them not wanting to get on the bad side of Nintendo because it used Libultra.

It's not only possible but I would argue highly likely that any LLM has absorbed that proprietary code into its training data making effectively any decomp not a clean room effort if they incorporate assistance from LLMs or coding agents into their tooling. If Nintendo wanted to be particularly onerous they could easily claim that their codebase makes use of proprietary tooling/knowledge and there would be zero recourse for the devs.

The term for that is byte-matching decompilation. This is not such project.