Im on sysnand with cfw all the time, since i have a legal copy of the game.
Also you can restore a save on syscfw, and go online without problem. Or at least on my case i havent had any issue
I dont think there is a code to increase spawn rate, but if u use poker to edit the spawn rate, if your son visit your island then yeah, he should be able to catch the fish more easily
I used pkhex on 3ds since US/UM, And on switch since SW/SH till now SC/VI and so far i havent been banned. Even if some pokes cant be placed on home, so far safe
I use jksv (same as checkpoint) to backup/restore saves and send to home. As long you use a legal game there shouldnt be any issue, even if you get the dlc pokemons without the dlc purchased
I have also some homebrew installed, and going online without any issue, I don't have any illegal game, everything was legally purchased and haven't got any issue so far