Games no, but if you've installed DLC via cia (important part) some games delete it when you go into the eShop, while others it doesn't affect them at all.
For example, the Smash Bros DLC is still installed and working fine on my N3DS with A9LH if I go into the eShop, but MiiPlaza games and Hyrule Warriors Legend's Season pass (both were sideloaded via CIA) are uninstalled and I need to re-install them each time I go into the eShop/update a game. Smash's DLC was also installed via CIA and has never had this problem.
tl;dr Your games (legit and CIA) and legit DLC will be unaffected. CIA installed DLC has a chance to delete itself if you visit the eShop and will need to be re-installed each time you visit the eShop (including updating games via eShop). This doesn't affect all games, but does affect some (which you'll have to find out yourself).