First of all how would you do this? You would have to reprogram the game, why? Well for one thing let examine how it works. The game is loaded, and checks the SD CARD for update and dlc. So just adding data to the complete package won't work. Unless you know how to actually make the game read extra data you inject into this CIA or ROM file, then its not possible.
Now perhaps maybe.... JUST MAYBE. Like how file replacement works on games, like how brawl mods work. It loads data off of SD when the game requires it instead of what is already on the disc, if you COULD SOMEHOW replace the data with in the game itself with either update or DLC data it MIGHT WORK. But since dlc is EXTRA DATA is not data you can replace, is completely new data, add on content. Which the game is naturally un aware of. Just like some updates add new data even though modify existing data. You may only be able to do Limited data, of updates. Which is the stuff that is labeled exactly the same
Now this is all theory, i never tested. Of course is just like rom injection, replace current rom with new rom to play injected game. You could in theory replace ONLY DATA that is similar or the same to make it work. BUT still the data that isn't same most likely extra data added to update, would not work. The update is required to use dlc for every game cause game normally do not handle the data as it is sold. It check for update data, load the patches, the patches contain instructions on handling DLC if dlc exist, DLC is loaded. No update data, no dlc. Only if the game was sold with instructions on handling dlc it could i guess not need update. But seem like new DLC need update.
Okay short story, theory it could be possible but is complicated. We seen games like Injustice ultimate edition with all DLC on the disc no update or extra download required but is done by the people who make games, not mod or hackers. No mod or hacker has ever try to insert dlc into a game, it was either created or custom data like mods and homebrew. Nintendo could maybe make Super smash bros, hyrule warriors or Fire emblem with ALL DLC on cart or as download. But maybe still it may even just unload and install it from game into appropriate file structure for 3DS games like it is now.