I'd imagine patches would be released via an internet update, Similarly to past Nintendo 3DS/Wii U games that released patches. Hypothetically speaking, The delay on the physical game release simply could have been to let people test the virtual copy for bugs, Meaning any patches made between now and the game's physical release could be pushed in to the game without the need for a patch. Those who currently have the virtual game copy will likely not have any problem updating, As opposed to someone with a physical game copy but no internet access.
Incredibly unlikely, I'm afraid. I've noticed there's been a lot of misconception surrounding the early release of the digitally-distributed copy of the game, so perhaps an explanation is in order.
First of all, physical distribution is a lot more time-consuming than people seem to realize. After the game has been completed, only then can the process of physical distribution begin, in which the game's ROM is flashed onto cartridges, packaged, and then delivered to retailers. This process can take upwards of a month, considering the sheer number of copies needed to meet the foreseen demand.
With these concepts in mind, I suspect that the physical version of the game is currently in this very process as we speak, preparing to be released as early as possible in the coming year. If this is the case, then modifying the ROM of the physical cartridges would require manufacturing to start
all over again, which would be expensive both in terms of monetary and temporal value. While it's of course not impossible that this could happen, I cannot imagine any business wishing to make a profit siding with such a decision.
Of course, it's entirely possible that an update to the game could be issued between now and the street date of release for the physical version, whenever that is. If this were to happen, however, both the digital and physical versions would be required to download it, for reasons of feasible practicality I've already noted. The version of the game flashed onto cartridges will be identical to the initial eShop release we have now.
Many have already made known their belief that the current digitally-distributed version is somehow an incomplete or 'rushed' version of the game. While I cannot dismiss the possibility completely, due to lack of evidence on my side to deny it, I would argue that the early release was provided simply to have the game available before Christmas. If the physical version is indeed in the process of manufacturing, this would mean that the game was already completed, with the only thing holding a digital release back would be waiting for physical copies to be created and delivered to appropriate retailers. You'll find that most games distributed both physically and digitally tend to release simultaneously so as one does not cannibalize the sales of the other. 505 Games likely made this decision with great care, finalizing this course of action so as not to miss Christmas sales waiting for physical cartridges to be prepared.