While in theory possible, just using cfw and homebrew as intended by the atmosphere devs,(Album or by holding R while starting another game), is normally safe for online use though.Any usage of CFW and/or homebrew can get you banned.
It's also how the atmosphere devs intend it to be used, and they go online in cfw themself.
Save game modification and cheating is dependend on the game though, if it's fully offline single player, it's normally safe, if it's using some type of online feature, it might be safe, or depend on what you do. It's also similar for mods offline safe, online depends and possibly not safe.
Nps and xci installations of any kind (even homebrew) is not safe though.