No
On the 3DS there is not any risk to get banned. So your are safe
The only way to get banned is if you download illegals copies of games using the eshop
Freeshop is dead, so you can use it anymoreSo only by downloading anything from freeshop and similar apps?
Any games that I already have from those apps are safe for online?
Freeshop is dead, so you can use it anymore
If you already have games installed then you are totally safe. If you want to install new ones you'll need to find the CIAs somewhere else and install them using FBI or a similar app.