Indexing adds a bit of overhead and thus consumes a bit more space. So a 100MB file that is indexed in DEVONthink will add overhead for the concordance (list of words found in the file) that DEVONthink creates in the background to aid search and other features. Size of the concordance depends on content of the file. DEVONthink makes the same concordance for imported files, so the net difference from a storage perspective should be close to zero. Of course, if you do not use DEVONthink at all, then there is no increased storage cost.
I suggest creating a small test database, index a subset of your folders, of known storage size (using Finder’s Get Info), and see how big the database is. Then create a second test database and import those files, and see how big the second test databases is. This will give you an idea of what will happen.
BUT – a few caveats. If you index files, and then start moving them around in the database, or start moving them around in the filesystem with Finder or something like it, then I find the best practice is as follows. Before you index, move all the files that are going to be indexed into a single parent file and index that parent. The indexing will cover all the child folders and files, and as long as you keep your reorganizing within that single parent file, you will not encounter the “missing files” syndrome in DEVONthink.
On the other hand, if your collection if files is not going to be referenced frequently, then putting them into a database is probably a waste of your time. Spotlight – or more sophisticated tools like FoxTrot – will serve you just fine.
The “index vs import” quandary has occupied hundreds of threads in the DEVONthink forum – which is a good place to go if you want from-the-horses-mouth advice. Indexing is a bit more reliable in DEVONthink 3 than DEVONthink 2, and is a very valid way of using DEVONthink. The discussion on which to use becomes rather talmudic and arcane – bottom line, again, is if you will not actually use those fines within DEVONthink, then do not bother.
IMO, DEVONthink makes a lousy archive if all you want is an archive – because you’re adding overhead that you will not be using.
Finally, some folks worry about lock-in with DEVONthink for files stored internally. Files are always stored in their native format; DEVONthink does not change files. And a hierarchy of DEVONthink groups including child groups and files can always be exported at any time, with the same structure in the file system that the hierarchy has in a DEVONthink database. Even at the worst worse case where DEVONthink hasn’t been maintained in years and macOS for some reason cannot run the software, the database itself is nothing but a bunch of files in a package folder, and your files can be retrieved – albeit the internal folder structure is not meaningful to you.