I don't think a system with digital versions of games would sell for more or the same than a system with the same physical game cartridges. Unless I can be proven wrong here in which case I will eat my words. Heck some stores even wipe all the content from the system, not that you can't just go to the e-shop and figure out what the previous owner downloaded and then download it again but most casual buyers do not know that. Stores do not take into account which games are on the system when you trade it in now do they? They don't give you more for a system that has 5 retail price digital downloads on it than they do for a system that is just a plain system, again, unless I am wrong here, but I know that GS does not take that into account when trading in systems. They don't give you the same value if you have a system with 5 digital games on it that they would give you if you had a system with 5 cartridge games.
Regardless all this digital stuff is just a bad investment especially at $30-40 a pop for games, unless you have tons of money to waste and a steady, well paying job that you will never be fired or laid off from or will end for some other reason. Because if something happens and you need cash quick and you want to sell your games you won't be able to sell them if you have digital versions, if you had the physical version you could flip your games for cash pretty quickly and sometimes a lot of cash, and it would not be a regret to have blown hundreds of dollars on digital games if you are now in financial trouble. With the prices of these digital games the money can add up much faster than you realize and before you know it you have a couple hundred sunk into digital games, games that cannot be recovered if your system gets lost or stolen.
If you plan on your 3DS working forever which it will not, buttons will wear out and batteries will need to be replaced eventually, if there are no replacements left on the market this will be a problem. Yes there is the transfer option but if the system dies totally and you are unable to do a transfer then you are theoretically screwed. Long term (20+ years) the 3DS will eventually become dead, and all your digital content will be gone, just gone. Whereas if you had a cartridge game you could at least either sell it off before the system became totally obsolete or purchase another system to play it on and easily slip the cartridge into the system and resume playing.