Nintendo respins hardware on their portable platforms all the time.
Gameboy/Gameboy Color, for example. I think there was a refresh of the Advance, and of course you had the DS, 3DS, and 2DS. I can totally see Nintendo releasing an updated Switch that's 100% software-compatible with the release model.
That is somewhat true, but they don't tend to change things up too drastically and its usually not a fast change. The DS Lite was years down the line though wasn't it? Looking it up guess it was a bit over a year. And it was mostly a form factor change. The DSi was years later and had a processor upgrade. The 3DS was form factor changes (XL and 2DS) for 3.5 years before changing the internals.
Which the move to X2 would probably be minimal, but I'm not sure I'd expect it terribly soon.
When their involvement was publicized Nvidia claimed that it was the start of a 10 years partnership. Also the TX1 in Switch has no customization at all. So my guess is Nintendo gets TX2 for comparable cheap sometime down the line when it's essentially worthless to Nvidia, just like TX1 was to them.
That was just Nvidia saying stuff and doesn't actually mean anything (JHH actually said two decades even...). I still have a hunch that Nvidia's chips are too expensive (with that being a big reason why the Switch is using the X1 instead of X2). The security issue with the X1 didn't please Nintendo.
The first version might not have been (even after Nvidia claimed it was...) but since they had to fix that hardware flaw they would've had to do a new production run (not really custom but that was more work Nvidia had to do). If it can just slot in without much if any change, I'd definitely see there being an X2 based Switch, or maybe they wait a while and release it with a bit of an overhaul of the design.
The real question will come when Nintendo is deciding on a new chip (don't think Nvidia has announced a consumer based newer Tegra chip?).
I wouldn't be totally shocked with Nintendo sticking with Nvidia, but we'll see. Nintendo is pretty fiscally conservative and tends to like having control. I think there were benefits to using an API made by someone else, but if Nvidia tries to hold that over them financially, it could become a problem. The thing is, if ARM keeps making progress, future versions might have GPU compatibility in line with the Tegra chips, making a transition away easier.
Even if they go with the X2, the CPU is still a bit lackluster, and while I'm sure Nvidia could make an updated one with newer ARM cores, it'd be about the cost. If another company could offer close to equal GPU performance with better CPU performance, for a lot less money, I think Nintendo might consider it.
IIRC rumors put the X1 at like $40-50 per chip for Nintendo. I'm pretty sure they can find someone to make an ARM chip for a lot less than that.