I have a region swapped 3ds and there aren't any downsides for me. You can still use multiplayer, and have an NNID and use the eshop despite what people will tell you. I forget that my 3ds is region swapped sometimes honestly. Here's how I got this all working for me:
Follow 3ds hacks guide but don't "install and delete" your downloaded cias just "install" them. Once you get done with that, follow their other guide to region swap, then perform a system format. Extended memory games (Pokémon ultra moon as an example) broke for me after the region swap, which a system format fixed. The system format also let me make a new NNID and use the eshop again. After that is when you would be reinstalling the cias that you conveniently didn't delete. Finally run TWLfix to fix your TWL firm which can break after region swapping.
That was just how I got everything working for me on my 3ds and in theory it should work for you too. As always, make sure you have a nand backup before region swapping or doing anything potentially risky.
Hopefully this is helpful for somebody lol xD
Also yes there is a new freeshop alternative checkout hshop.