Thanks for the replies!
I should have given more details. The "major reason" I want to enable 3d acceleration is that it renders the "fog of war" differently. Using the widescreen patch causes software-rendered fog of war to flicker like a strobe light when the screen scrolls.
I disabled transparent shadows to no avail, thanks for the suggestion though. I will continue looking for solutions and will post again if I find one.
EDIT: so...for what it's worth, i've found that the flickering only occurs at 1280 by XXX resolutions on my computer. 1024x768 does not flicker. So I guess I'll be playing this game with black bars on the side. It's a small point, but it's soooooooooo frustrating that a game engine would implement opengl so badly that it still has performance issues 12 years later.
It's probably not the games fault as much as modern video drivers. Features become deprecated or even worse can be completely removed, like ATI has done with some features that were popular 10 years ago but no longer used now. We are probably lucky OpenGL mode still works at all.