Welcome to the internet.
Serious answer to the OP: you can usually find CIA's and DLC's from that iso site. You can use those to update if the eShop isn't working. From my experience, a lot of titles will update from the eShop directly, as long as they are the same region as your 3DS or are region free.
Edit: I personally like to stick to downloading the updates in CIA format whenever I can, as I feel kind of bad for using the Nintendo Servers as I haven't paid anything for the games. This is also why I don't use tickets.