'Mappers' are just a name given to extra hardware in the cartridges, usually to provide functionality that wouldn't normally be possible. This can range from simple extended ROM/RAM capacity to much more complex hardware, even additional sound chips and the like. (and on the SNES, things like the SuperFX chip)
'hacking' a mapper in the sense you're talking about would involve rewriting parts of the game code, and if nothing with similar capabilities was available, downgrading the game in the process.
even when it's a simple case of ROM/RAM banking it can be a significant undertaking to catch every piece of game code that relies on banked data and change it to work with another type of mapper, risking introducing bugs in the process.
it's a lot of effort just to make things run with an inferior, buggy, incomplete emulator just because that emulator was provided by Nintendo.