I think the only possible downside is if you use the dump and the cart at the same time on two different switches.
(offline play might be ok for this though)
It's a similar situation to the 3ds carts, if the unique header from one game is being used in two different instances at the same time, then it would be blatant that one of you was being a dirty pirate.
Like if you dumped your games, then sold them and played the dumps online.
I'm not 100% sure though, but from my experince with 3ds, and the fact that there is unique info in each switch cart, I imagine it'll be a pretty similar situation.
So assuming you aren't going online on the dumped nsp (which, Ninty server connection = ban isn't pretty much all cases in the first place) then yeah you "should" be fine.
If the games are not both going online at the same time, especially not the dump on the hacked unit, then I don't see how there can be a problem. (I know botw isn't really online, but just play it safe)