Is there a story behind the Doom Guy dolls?

They are really just collectibles for going off and checking out all corners of the maps. The same for the retro Doom levels, they are just a nice secret area to hunt out.

However the DoomWiki does have a small (very small) exert as to their possible inclusion.

The Doomguy collectible is an approximately nine-inch-tall action figure, evidently created by the UAC to venerate or to celebrate finding the Doom Slayer.

Side bar: As for the research base / scientists not wanting to wake the Doom Slayer, well I think that's more Hell that didn't want to wake him based on the chilling tales within the game of how he nearly brought Hell to it's knees.

Doomguy Collectible