I've never heard of these issues myself, and searching on Google doesn't seem to bring up anything.I remember seeing something about Pokebank interfering with cia's and homebrew. I have RxTools on an O3DS. If I open Pokebank does it actually damage some of the homebrew I have? :c
I would say it should be safe to use PokeBank without causing any damage to your Homebrew. I can't think of any reason PokeBank would cause an issue.