Cyan, got the publishing rights, back from Ubisoft, for all their games, and are the source of those released on GOG.
Myst 3, and 4 were not made by Cyan, and they had no rights to those games, so they are not included in the package.

As for Ubisoft putting them on GOG, frankly there's little chance of it happenning.
Uplay has a section called Oldies But Goodies which is almost a game for game match for the Ubisoft games on GOG.

There's a good chance, that no source codes available, or other rights licenses used have expired.
If Ubisoft could release these games once more, they would be already on Uplay, and then have a good chance to be on GOG as well. Without a Uplay release, there won't be a GOG version.

Sad fact is, until GOG appeared, nobody thought old games had any value, and though publishers would keep the IP, the source code for old games, often wasn't thought worth keeping. Many GOG resurrections, are because someone (usually a developer) kept the source, out of nostalgia.

Homeworld Remastered is an example, it doesn't contain Homeworld Cataclysm, because the source code has been lost.