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It's completely valid to think about. Note taking programs inherently come with a "technical debt." The more you make use of its exclusive features the harder it'll get to transfer.
If you're worried about migrating I'd recommend something open source or self hosted. You can always choose to stay on a specific version you know will be easy to migrate from in needed.
I used Notion for a while in like 2020, it was fairly easy to transfer to Joplin, Obsidian, and later Logseq once I decided to move to more source available options. But I imagine with how many features they've added it might not be as easy anymore.
I'm currently exclusively using Logseq markdown, the one pro but also con is the non-linear note storage. Every page is in a single folder and they're linked using tags and references rather than organized by folder. Super intuitive in Logseq and it works with other markdown editors like Obsidian too, but open it up in a regular file explorer and it looks like a mess lol.
currently in obsidian and wondering abt logseq. as a sw eng myself i kind of like “its just markdown” anyway. i don’t share, collab, or really do much more than some data table js but thats it.
but having each note be its own folder seems… weird.
Actually it's all in a single folder. if you want it sorted into folders you have to do so manually in a external application or use a plugin. Sorry for the misunderstanding.