Why????

There are too many of them to list them all here.

Sure, I can always extract the files from the Windows version and play them with DosBox or SCUMMVM on Linux, but why, GOG?

It is a rather fake restriction, possibly done on request of the publisher, or possibly just apathy. Another group of games that could now have a native Linux build are AGS (Adventure Game Studio games like Ben There Dan That, Downfall (original non Redux), Kathy Rain (original), Time Gentlemen Please, etc, due to ScummVM adding native support for AGS since v2.5. And ResidualVM games (like The Longest Journey, original Grim Fandango, etc) whose support was also added to ScummVM in v2.3 are also eligible for a native Linux build.

As annoying as it is though, to be honest I've always found it more convenient to "DIY" them as collections, ie, install all DOS games one per subfolder under one \DOS folder using just one central DOSBox then zip the whole lot up at once. Reinstalling is much faster than installing each game one by one using GOG installers if you like to have a lot of games installed (and is needed anyway for non GOG games). Likewise it retains custom key-binding between installs (eg, if you use the DOSBox CTRL-F1 remap feature to add controller support for an old platformer, etc).

Basically they are still DOS versions (or Amiga or FM Towns or ...).

The technical solution with ScummVM works of course for other systems as well, it's probably a licence thing.
But yeah, if GOG could manage to convince the rights holders that they are allowed to release them for other (so far unsupported) operating systems, that would be great.

I think what GOG could do to avoid legal issue would be to create an add on, that extracts the files from the windows installer. One would probably work for all scumm based games, but it would have to be able to distinguish betwen scummvm games and others.
A better solution might be a patcher that replaces the scummvm, like you did manually.

And an even more elegant solution would be a "Just the data files, please" so we could hand assemble things our way, instead of having 100 redundant copies of Dosbox. They can't even keep up to date, so why not?