I’ve looked at how applications such as Eagle Filer, Keep It, and also apps such as nvAlt, Evernote, Bear, Apple Notes, etc store the files. In general I regard the options presented by DEVONthink much better than Evernote for instance in this regard, though it of course depends on how you use it.
For instance, if you create Markdown files, pdfs, images, rich text, formatted notes, rich text, etc in DEVONthink, you can find the actual files on the file system if you navigate inside the
.dtBase2 database (which is actually a directory). So this means that you can can for instance modify the files directly with external applications; that is, you can modify a Markdown files with a text editor or a PDF file with Apple Preview just like if they were on the file filesystem. You can’t for instance do this with Evernote, Bear or Apple Notes notes. In the case you didn’t have any access to DEVONthink after some years, but had the
.dtBase2 package/directory, it would still be quite easy to get the files out from there without specific tools.
Getting the folder structure, tags and metadata out might require more work, though at least if you have access to DEVONthink, it plays quite well with MacOS concepts when exporting, etc. For instance there’s a more complex option to “index” a regular directory with DEVONthink, which option seems to sync for instance DEVONthink tags and Finder comments with the MacOS tags and comments. Also, for instance the encrypted databases are actually the same encrypted disk images that MacOS uses, so you can quite easily open them with Disk Utility or Finder if you just maybe rename the extension of the database.
If you collect a lot of DEVONthink specific custom metadata, annotations and things like that and they’re very important, then you may want to look at also how to export them to another system. However, this is also the kind of data that Eagle Filer or Keep It don’t support as such. However, I think if you have just something like a regular file system folder with maybe Eagle Filer or nvAlt (or upcoming nvUltra), it may be much easier to for instance apply different backup solutions, sync and access with different apps with something like Dropbox or iCloud Drive, restore earlier versions with Dropbox, etc. The encrypted sync stores in DEVONthink is a good thing, but besides that the perfomance and reliability issues with DEVONthink’s sync solution is one reason I’m still using or looking for other alternatives for some things.