Maybe. There are many ways to move files and directories around without using Finder, at which point all indexed data about those files and directories will be stale. Forcing something as core as mv to update Spotlight would be significantly worse, I think. By keeping the .DS_Store files co-located with the directory they index, moving a directory does not invalidate the index data (though moving a file without using Finder still does). Whether retaining indexing on directory moves is a compelling enough reason to force the files everywhere is probably dependent on whether that’s a common enough pattern among workflows of users, and whether spotlight performance would suffer drastically if it were reliant on a central store not resilient against such moves.

So, it’s probably a shaky reason at best.

If dropping a database scares you, you are either unaware of the disaster recovery process, or there isn’t one. Edumacate yourself, or the org, as appropriate, so as to increase your confidence when dropping databases.