In short, are the short-term gains from using whatever fancy, proprietary features in a tool worth the cost of spending time worrying about lock-in, and the lost time or lost search results when you can't query all of your notes at once?
Again, I think this comes down to how and when the notes are most useful. For things like my Daybook, I'm convinced that simple text files (Org mode, in my case) are best. They're mostly for searching later. Sometimes much later. No other features are necessary to get value from my notes.
But for, say, notes about an active project, features such as transclusion and backlinking and spatial presentation can be very useful and totally worth the trade-off of (maybe) being "broken" some day in the future. I have notes from many defunct apps that can still search in a pinch. Voodoopad, Circus Ponies, etc. I just made sure to export them as best I could when it became obvious the software was going away. Spotlight almost always finds what I was looking for. It's not ideal, but it's not a big problem, either. Sure, I lost the fancy bits in translation, but I no longer need those features for those notes. As long as the fancy stuff is just layered over extractable plain text, it's probably never going to be an issue. Stop wasting time hand-wringing and get on with it, I say 😁.
What about my "Second Brain" or "Digital Garden" or "Zettelkastan" or whatever the Productivity Bloggers are labeling their random pile of notes these days? This falls somewhere between needing to be useful now and remaining useful forever, so it muddies things a little. I'm convinced that if one is trying to (lord help me) "synthesize knowledge" from their notes, the extra organization or presentation features are in every way superior today to a wall of plain text notes. Why not take advantage of it all?
(Of course, I use plain text Org files for nearly all my personal notes, but that's not because I fear lock-in. It's because I love Org mode so much.)