The final official Nestopia depreciated mapper 23, using hashes to support known (thus official, unhacked) games. I am well aware because it was just after I released a translation patch for Dragon Scroll and got people complaining it didn't work on Nestopia, which I had previously tested it with (on a version prior to the anti-23 code).
I would say it was too late to try to untangle the mess of Konami VRC2/4 variations.
I had that problem recently with Kid Dracula. I think it's still possible to play it in Nestopia if you soft patch the ROM instead of hard patching it. Meaning, put the patch and original Japanese ROM in the same folder and then load them from Nestopia that way. It worked for me with Kid Dracula.
May the Dragon Force be with you.
That was the other big one that didn't work for me on Nestopia, yeah. FCEUX seems to be working fine so far, so I'd recommend going with that.