When I used to own the game back in the day, there were a couple of puzzles that required the manual - as a primitive form of copy protection. Have these puzzles been removed?

I don't have the GOG release, but I would be surprised if they had removed it. It is part of the game play. The needed information is in the PDF manual.

I can say for sure they have not removed it.

I'd be really surprised, if the copyprotection would be gone. I don't recall Sierra doing that even with CD releases of their games. I have KQ6 on a Robeta Williams CD collection and all games in that one got copyprotection in place.

Sierra did remove the copy protection that was on some of the floppy versions on some CD games like KQ5 and LB2.

I've never played floppy version of KQ5 or LB2, so I have to trust on your word about that.
In those games the copyprotection isn't propably integrated as gameplay though, like in KQ6 and KQ3. On both of those games you need the manual to do specific tasks, like the magic spells in KQ3 and if I recall right, the cliff puzzle in KQ6.

You can actually figure out the cliff puzzle without the Guide Book. It's not very effective as far as copy protection goes.

The puzzles are still there - and you can get a copy of the manual from your download page on gog.com.