I'm not sure I follow what you mean, if you install the game under sysNAND first, then install it again under emuMMC it won't remove the original menu entry from your sysnand, it will just add one to your emuMMC and rewrite all the data in the Nintendo folder. But how would you install a legit eshop game on your emuMMC since I assume you won't connect to your account there ? If you made backups of your legit games (assuming there is a tool for that) and the backup tool handles tickets properly it should be fine but I'm not sure and i wouldn't risk it personally. If you wan't to be 100% sure to keep your sysNAND clean I would definitely advise keeping separate Nintendo folders and just investing on a big sd card (you can get 256Go for like 40€).
Yeah, thats what i mean, if for example i download this backup online instead of dumping it by myself, and this backup is slightly different (for example i have the cartridge version VS i download NSP version or an XCI badly converted to NSP). I can't never be sure that the game is 100% exactly like the original i have, so when i go back to SYSNAND and go online i could be banned even if i have the original game, because of installing a copy with your method. So as i don't want to be banned i guess this is not a good solution and the best thing would be to just have the game duplicated in both partitions.
I know goldleaf and read the "Nintendo" folders where the games are stored but i can't seem to launch the games from there. It would be probably possible with a future homebrew that uses a "READ ONLY" mode on the SYSNAND to read the contents of a game and virtually linking it to an emuMMC "fake game container".
Anyway its getting too complicated and im not here to create this Homebrew, i was just asking if it already exists, so i will stick with the normal method!