Literally not freeShop's problem.I said the apps not illegal but most people are going to use it to pirate. If you legit bought the game you can just redownload it though the real e-shop if its digital or dump it if its a hard copy and dumping the game may be faster depending on your internet speed.
I personally use freeShop to get updates for my games. I don't like how Nintendo handles their updates. It's either extremely in the way (prompting me when I am trying to launch my game) or annoying to get to through the eShop. freeShop, I just go to a tab an all of my updates are right there.
I also like the simple setup for redownloading my games. I find redownloading my large games like Smash tends to crash when going through the eShop and not in sleep mode. Something I don't find happening with freeShop.