Short version. Yes, unless you keep it offline in the hope that a future hack set will be able to make it look all shiny and legit, or take a backup of the legit version, play offline in hacked mode and restore the legit version later (probably also making new legit versions as it becomes necessary), then go offline in hacked version....
Longer version. Nintendo has been shown to be playing for keeps and are employing complicated high end security as part of it all; this is new for them but indisputable that it is happening. Right now they may not be employing certain checks, or banning for failing certain checks, but the only sensible play in a game theory/battle plan sense is that it is there and to plan accordingly.
Anybody saying [blah] is safe (barring the offline methods described above) is either a fool or not playing the long game. There is a line of thought that says you might get away with certain firmwares if you know only certain checks are done, however "any" update (possibly even any new game or update to one) will realistically see you either diff a firmware to see what changed (for every region no less) or have to re-evaluate. Cable/satellite box companies famously used to have lots of rapid updates on their models to frustrate hackers here and Nintendo could do something similar here if they wanted. Alternatively it might be possible in the future to have a donor switch provide its keys to you to pretend to be another device (see something like 360 key vaults or localfriendcodeseed_b for the 3ds, I assume Nintendo are not stupid enough to do something like the mac bans for the Wii and DS again which were trivially changed locally and did not have a server side list) but that still means a ban, and likely paying someone for a donor set of keys (we shall leave the more black hat methods alone for now).
We have control of early boot on the Switch (or at least enough of them that you will likely be able to find one as long as the online service is viable). In the future as mentioned earlier we will probably have an emulated NAND type option. This will either be used for dual boot to allow people to keep a hacked one offline or mask the hacked version such that it can't be traced back to your serial/keys (which may be easier said than done, and does come with some downsides like what if a hacked save appears on your legit side).
Further in the future then as we have the levels of control we do then someone could go through the firmware, find all the checks Nintendo employ (and it is not necessarily going to be easy -- see obfuscation), possibly be a bit limiting (security can limit things you can do -- the 360 notably employed encrypted memory which makes dynamic recompilation, a favoured method of emulators for post 16 bit era devices, very very hard, hacks them granted a window of unencrypted memory which could be used for that but stuck out like a sore thumb. Going with Nintendo then something not altogether dissimilar saw their javascript engine be slow as sin and thus the browser rather limited in capability compared to what the hardware could probably have pulled off*) and build accordingly. Nobody doing any kind of custom firmware thus far has remotely indicated that they care to play find a check, much less shown they are doing it properly (and for my money what they would have to show is akin to some of the sophistication we see anti malware people employ) and other than TX I would possibly even put some money on the makers of such things not caring to do that on some kind of principle and if not that then apathy.
*it should be noted though that the 3ds had long been surpassed by phones, and in some ways had been surpassed almost from the start -- the stagnation in phone/tablet specs had not yet hit when the 3ds did).
You also have the possibility a homebrew online equivalent will be made. I don't know that I have seen a full one while consoles are active before but I am not going to rule it out entirely, however firing local play over VPNs has been a thing in the past and might be an option here (and unlike most other devices they do appear to have some what would traditionally be known as LAN play games) and the option for a VNC type play (kaillera if you wanted a name of a service popular in games) is also being discussed and has been seen officially for the PS4 and xbone.
Some seem to be of the opinion that an offline console is as good as a banned console (possibly even worse as people have not really got off their arses and set up a game update or even console update sharing service yet). I view this as short sighted. I would say short term pain for long term gain but... it is online current Nintendo online. The fly buzzing around my room right now is probably more annoying to you than losing Nintendo online in the short term.
