99% of the time (I rounded down) it's because of a licensing issue. Possibly the CD version had music that was licensed to be distributed for a certain amount of time or copies. Or the CD version was only authorized in certain countries and not worldwide.

So, GOG's awesome team of awesomenauts have to hunt for people to sign new agreements. If they do, then Great! You have the full CD version. If not, poopoo! Just plain old disks.

(NOTE: The following is from 10 year old memory anagrams. Take it with a grain of salt.)
As for the original M+M files, there would be no need for cracking. So they shouldn't be cracked. However, the files on the 6-pack were altered from the originals in a small way. The disks were given directories and the game would call from those directories to load up the maps.

Several of the old-school versions came on several floppies that had to be swapped. 512KB just wasn't enough space.

As for the CD-version ones (like MM6), I don't know. I'd bet they were cracked. But I'm not sure.

Your best bet would be to buy the games from ebay and do some backing-up that way. If the archiving process is extremely important to you, I'd imagine it would be a small price to pay to keep the original files preserved until the end of time.

That said, the end of time is Friday. So you'd better pay extra for expedited shipping.