For what it's worth, even with my 3DS being banned from the eShop and from NNID services (and the workaround to get back online done, of course), I've never had any trouble updating 3DS games, either installed directly from cia files with FBI or downloaded with the freeShop fork, using the automatic update option offered on apps in the Home Menu. The only time I've ever had to grab an update from ~that ISO site~ has been with All Kamen Rider: Rider Revolution, because that wasn't on my region's eShop in the first place.