I wonder if they will make changes for the second batch to help prevent hacking. My guess is no because it would be a waste of time. Nothing prevents hacking. You can only delay it.
However, it's more likely that there will be some type of difference that forces some people to try and collect the variants. I'm also curious if there will still be some demand for the "original print" units.
Definitely can't seem them changing it, since they've already made it really clear that these classic consoles are not high on their priority list. Like you said, hacking is inevitable, and they surely know that.
I'm curious about this myself, especially considering they are currently still available via several Chinese vendors, made from the same parts/materials, in the same factory. Which also makes me wonder about Nintendo's possible role in the bootleg consoles. They haven't shut them down, which is quite shocking considering that they're 1/1 perfect clones...