Pirate games with odd mappers?!

I can't be sure, but my guess is that the manufacturers don't have access to any official mapper chips, and care more about having a cheap/easy to manufacture device than sticking to standards. They'd probably rather hack a game to use a cheap mapper than use a more expensive mapper that's compatible with existing code.

As for why emulators don't support them, I'd imagine that it's probably because most people who have them lack the hardware, knowledge, or inclination to dump them and document the mapper hardware.