Without rehashing the whole sorry saga, of my DEVONThink corruption, I lost both imported and indexed files.
As to whether backup software sees packages as single files or folders I would think that most will see them as folders but not sure.
bit rot also includes the case of multiple copies of a file being made and errors in the transcrition creeping in so periodic bit by bit verification that the copy you just made is an exact duplicate fo the one you started with is in order for important data.
And by the way, not to overcomplicate this too much, but there are also two different types of “database” to consider.
The first is what you’re using - a database that contains information about separate files, like DEVONthink. If that’s all you care about, you can stop reading.
But an app doesn’t have to store notes as separate files, which brings us to the second type of database. For example, Bear stores everything in an SQLite database. That’s a database, but for an app like that, what you likely think of as “files” (i.e. “individual notes”) are actually just pieces/parts of one big file, which would make them much more vulnerable to potential corruption.
Bottom line? If your data is hugely important, you always want to know what your app is doing with your data, so you can plan accordingly.
My bottom line would be: everything else being the same, better to use standalone files. But is everything else the same? There are portability, backup, workflow, and capability considerations that are much more important than the integrity concern by itself.
