I think there might be in some cases legal reasons if they don't have the licence for it and they can't just take it even if it's available on the net (even replacement docs say what they do is not strictly legal). However it looks like in some cases it's just sloppiness. For one thing, surely if the manual is available in the game folder, then there is no reason to add it to the extras too.

I'll see if I can contact support about this.
Nirth confirmed it.

https://www.gog.com/forum/anno_series/could_anyone_please_confirm_anno_1503_has_pdf_manual_in_game_folder/page1

Update:
Added to my gogmix a link to the typed-in Amiga version of the manual of Patrician 1, which was also missing, as well as the French manual and quick reference.

edit-also since I was at it, I found out that the manual for Police Quest SWAT 2 was missing and added a link to it in my gogmix

Added more from the GOGmix.

Added more stuff from the GOGmix, plus some question if anyone can answer (regarding Metro and Crimzon Clover).

Was there a physical pc copy of either redux?

No idea to be honest.

Yes.

Thanks. The question then is whether they had a separate manual, because the ones we have links to are for the non-Redux version only.

From the vibe I'm getting through my Google-Fu skills, the Redux versions have no manual at all. At the very least, the PS4 version had none. Extra note that the Metro Redux games were only sold as a bundle in a physical form. Crimzon Clover did have a [url=http://www.ebay.com/itm/PC-GAME-Crimzon-Clover-STG-Shooting-/271727031237?hash=item3f443173c5:g:MSQAAOSwc0FUpWrH]physical release[/url], but only in Japan.

OK, I'll keep them on the list, since the non-Redux manuals are basically the manuals for the games and should be included anyway.
I'll keep the question open in case someone could make a 100% confirmation, that the PC Redux bundles had no additional PC manuals either.

... which means there wasn't ever an English language physical manual, right? In that case I'll keep it off my list.

I had been putting this off lately because I was kind of busy with other stuff and also wasn't certain if the resource I found fits the definition of a manual but here goes:
Added to my gogmix:
Grim Dawn -A game guide having sections similar to a manual can be found at the game's own website at: http://www.grimdawn.com/game.php

Let me know in case there's any problem with that resource...

Yup. That unofficial translation you had above is the closest thing we had to an English manual.

I just noticed Trine is included in the GOGmix, but its store page mentions that a manual is included:
https://www.gog.com/game/trine_enchanted_edition

Could someone who owns the game clarify, please?

Yep, manual is availabe as extra :-)

Thanks.
Treasure, you might want to remove it from the GOGmix.

Also, I've put the Trine 2 manual up here: (the link in the GOGmix is an ftp with a suspicious "torrent" in its name)

https://www.dropbox.com/s/358bxa36yfg19sa/Manual_English.pdf