Let me put it this way, .DS_Store is just the new form of the Desktop files we are so used to being annoyed with under OS 9, just in a method that *nix GUIs seem to do.
These issues of hidden files popping up is definitely not new, you try sharing your main boot drive using FTP or something and watch all the OS 9 crap show up like 'Desktop DB' and 'Desktop DF'. There was a reason for this switch, but Apple has not taken the time to explain it to the "common user".
One of the reasons is that it is a little easier to work with drives suffering from fragmentation when you don't have your constantly changing database locked down to one file strewn all over your HD's platters.
The other reason is it makes it easier to move the metadata from one machine to another. If I burn a CD or make a stuffit archive of a folder, all the metadata is assured to go with it, including which app to open the files inside with. You don't get this with Stuffit archives all the time, so comments, etc may be lost. If Apple wants to expand the current .DS_Store structure, they can, and still retain the mobility of that extra metadata.
Plus, what if your HD crashes and you need to do a recover, or inodes corrupt and you start losing folders that you can't recover for one reason or another? With a centralized DB, you lose out if it is all attached to a single location and that DB dies. You get extra excess entries that are invalid if you lose inodes (folders).
I personally think .DS_Store is a better mechanism than the older Desktop structure. We still have the issue of FTP servers that show hidden files by default, but that is the FTP server's issue, not the OS'.