To your first question - once you've disabled the plugin you would only be able to build your hunting grounds and ruby mine, not your crystal mine and cabbage patch.
To your other questions:
1) no, the only things that can get you banned from online (i.e. no one can visit your castle and you can't participate in online battles) is having enemy only weapons, dragonskin, or too many characters in special (nohr/hoshido prince/ess, foxes, wolves, dancer) classes and then updating data. that's it.
2) Just google it dude, I can't hand hold you all the way. Download the plugin here: https://gbatemp.net/threads/request-fire-emblem-fates-special-edition-usa-cheat-plugin.415563/ or here: https://gbatemp.net/threads/ntr-cheats-plugin-ported-from-gateshark.427187/
Download the 3.2 NTR.bin here: https://github.com/44670/BootNTR/releases
and shadowtrance's 3.3 bootntr.cia here: https://github.com/Shadowtrance/BootNTR/releases
put the plugin in plugins/titleID, run bootntr.cia, run fates, press x+y.
Make sure you're using the ntr firm for Luma 3ds on the luma wiki.