I remember discussion at the time about how the PS3 was a uniquely difficult architecture to emulate. Was that true? Have those difficulties now been overcome? I see RPCS3 exists but I’ve no idea if it has done the difficult parts.
Depends on your definition of "overcome". RPCS3 does emulate the architecture, and many games are playable on it, but it's still far from being perfect. Many games have stability issues due to timing/synchronization inaccuracies, for example.
I believe the PS3 was designed to make it difficult to emulate.
Why go through the pain to design such thing, which makes it difficult for developers, while I don't think it would really result in better performance.