If you bought many games from GOG you probably are using a crack.
Pricne of Persia Two thrones, for example, is most definitely using a crack by Reloaded. There is no attempt t hide this.
Now the original PC version has some pretty nasty Starforce DRM in it. Rather difficult to remove.
Did gog.com themselves grab the crack? Probably not. Did the publisher not have a de drmed version, and simply take the working scene crack? Most likely.
When the publisher has an actual without the DRM version of the game, they are likely to use that. But that's simply not always practical. Sometimes the protection is so heavily integrated before the final version of the game is made, that they simply can't get a clean version of the code.And they naturally try to make it as difficult as possible to remove the DRM so it actually works to stop piracy.
So why reinvent the wheel if someone has gone through all the hard work? A crack cannot actually be copyrighted, so the scene group may bitch all they want, but there's nothing they can really do. Publishers have grabbed scene cracks and released them as patches for their own games before gog.com existed, and they are likely to continue to do so. And it's not actually wrong for them to do so.
Sometime when you are bored, compare files between gog.com versions, and existing n CD patches. You might be surprized.