Really, how hard would it have been to add a protective layer over the top? Is there any substantiated reason why they don't?

Actually, they're supposed to coat the top with something. Almost all of the CDs I own have the top coated with, at the very least, a layer of silkscreen ink as part of the labeling process. This is usually enough.

However, I have a couple CDs in my collection which don't have this coating and the silkscreen ink is just the lettering without any ink background (not even transparent ink). So these started skipping eventually because of the scratches induced by my slot-loading car CD player.

Oddly, they were both B-52s CDs. It wasn't until I got into ripping and MP3s that I was able to recover them. The error correction in most of the digital audio extraction programs is enough to get around the skips induced by the scratches. I was able to burn fresh CDs from the extracted WAV files.