I have an old pc lying around that still runs windows 98.

I wanted to replay Monkey Island 3 on it direcly, without using scummvm, but I cannot find any .exe executable
or similar among the files instaled by gog.

Is gog version stripped down so only scummvm can play it or is there something I can do to get it running on my old machine?

Most GOG games that use ScummVM only have the files necessary to run it with ScummVM (see https://wiki.scummvm.org/index.php/Datafiles)

You will see a topic pop up every now and then about how they should include all game files to be able to play the games in the original hardware and OSs they were made for, but so far there's been no response in words or actions from GOG.