Not really. It’s a pretty straightforward story when you get past the spectacle. Really the vast majority of the movie is 2 people and a computer, not a lot of complexity there. Mythological mysteries that never get answered aren’t complexity, they’re contemplation points. To me if you want complexity you usually need to head to heist or scam movie. That’s where plots get complex. Most movies are rather linear.
2001 was abstract in a way that was unprecedented for an American studio film. The visual style or “spectacle” conveys the themes so you can’t really ignore it. You’re saying that only a plot can be complex and not over arching themes?