If you have the storage space to do it, and feel like spending several hours (depending on how many games you have) you could. There is always that iso site and ciangel/freeshop though... If you are afraid of losing games though, just keep backups of your save files every once in a while
I once lost my pocket of 3DS games for a full year! I misplaced it like I usually did, so I thought "no worries, I have plenty to play digitally on my 3DS" (as I've downloaded a couple full retail games from the eShop). Then when I wanted to go back and play some old games, I searched everywhere and I couldn't find it! And then we moved! Seeing as I had lost it for so long, seeing as we had moved, with all these factors, I abandoned all hope of finding it (my precious Pokemon X!), until one day... I found it in a random backpack in the garage! Man, you don't know how happy I was then!
I had lost it once before, too, under the seat in my car. That was a whole month right there xD
I think I might do what you're planning on doing and back up my games in case I go full dumbass again, haha
If you don't want the fear of losing all your games and saves, you should dump them if you have the space to on your sd card. If you don't that's fine too.
Some people prefer the feel of actually inserting the cartridge rather than just tapping on an icon anytime you want to play a game. I would just back up your games/saves onto your computer or external hard drive if you have one though just in case.