Except for the transparent aluminum screen on earth of the past, I thought they were all done traditionally, with conventional animation, not via computer at all.
On TUC, Cimiti Arts handled the graphics and only a small portion of those were digital (I remember a thread here once that discussed how the screen graphics of the Enterprise were CG.) According to associate producer Brooke Breton, Barbara Cimiti had done screens for previous films.
I think Breton's association with Trek may date back to TVH (she was on season 1 of TNG for sure), so if anybody knows if Cimiti Arts exists in any fashion these days, that might be who to contact.
EDIT ADDON: I could believe the Atari reference if you're talking SFS and the GRISSOM graphics of Genesis planet, which looked incredibly crude. I'm pretty sure all of the SFS stuff was done by companies who just wanted screen credit, so they were fast freebies.