You can find each and every homebrew on the internet and transfer it to your switch manually. Or you can use atmosphere's prodinfo blanking to hide your console's personal info and stuff. That way you can safely use ftp and other stuff like accessing hb store (you won't be able to connect to ninty's servers of course).
You can use Incognito, 90DNS, and as said above I think atmosphere already can blank prodinfo just like Incognito but without really deleting it. This is only "safe" if you're using Emunand though, because you really don't want to go online after using CFW on Sysnand.