I think something that kind of gets overlooked when discussing Nintendo's questionable preservation practices is that, internally, they (generally) seem to be pretty top-notch nowadays - leaks and official releases alike (like Sakurai's Creating Games channel!) have indicated that a lot of pretty important pieces of development history are still accessible, and I imagine it's unlikely we're ever to likely find Nintendo in a situation similar to their disputed ownership over Joy Mech Fight because of a misplacing of documentation again. (Also, how the hell did Nintendo manage to just lose the rights to a franchise for like, 20 years, by literally just losing a document?? That's hilarious to me, not gonna lie.)
I think the actual problem is more of an availability issue, in that they don't want the unwashed masses to get access to stuff that isn't public-facing. On the one hand, I can sort of understand the thought process, and recognise that there may potentially be issues with what can and can't be shared about development... but at the same time, the game designer in me really would love to see them release entire GDDs or ROMs of their development titles. I don't know about you, but I'd kill to get my hands on accurately translated GDDs for the entire Smash series! (Well, metaphorically... unless?~)