Note that the ranges of Date Created and Date Modified can also be useful for comparison of states of a database over time. As most of my databases incorporate notes that I’ve created in the database and frequent Web captures, Date Created sorts are pretty good distinguishers of differences over time.
If you wish do to absolute comparisons of database contents over time, it’s possible to create plain text lists of all documents within a database. To do that, Either in the History view or in a smart group that lists all documents, select all and copy to the clipboard. Past the clipboard contents into a new plain text document. For example, I could create a list of the more than 30,000 documents in my Main research database, and compare the list to a similar list of an earlier state from a Time Machine backup. There are third-party applications that allow one to compare two such documents and identify their differences, which you could find by a Google search. (Your initial proposal of making backups of Files.noindex would likewise benefit from such a comparison of filename lists, and would simply add another complication to keeping backups, so isn’t recommended.)
You mentioned that you have 16 “versions” of your database, including Time Machine backups. I’ve got many more than that, as I’ve got years of Time Machine backups, as well as a number of Database Archive backups. That’s a Good Thing, not a Bad Thing.
My most used databases are modified very frequently, adding new content and sometimes removing or archiving from the database obsolete content. Sometimes I rename documents, especially scanned documents, after capture to a database.
Caution: If you start restoring backups to compare their contents with your current database, don’t get confused about what the current database is! Before restoring older states of the database, I always zip the current database file (important – close the database first). After restoring earlier backups (which will of course replace the current database), I can always return to my current database simply by deleting any older version and unzipping the current database.
I’ve never had a problem with files going missing from my own databases. I’ve been using DEVONthink heavily for 13 years now. I attribute my database reliability to maintaining good habits including periodic checks using Verify & Repair to make sure the databases are sound and also that sound backups are being kept, and to keeping the computer and its operating system sound by preventive maintenance routines. I haven’t had an error report by Verify & Repair in a long time, probably a couple of years. I haven’t had to resort to a database backup because of damage, for more than 5 years. My current late 2012 MacBook Pro Retina has been a delight. But if I had not followed preventive maintenance, especially periodic checks of the Disk Utility Verify Disk procedure, I would probably have had serious data integrity problems not only for my DEVONthink data but everything else. I’ve had to correct SSD disk errors 7 times. Had I never checked, I suspect I would have experienced a crashed disk – and before that happened, my computer might will have lost or overwritten files on the computer.