In case you weren't joking about the multi-core thing (there've been a number of wall-of-text-wars on that one), no, there's no general multi-coring due to the nature of lock-step-sync RTS games like this one. The AI runs in a separate thread (on the host only, as clients don't have any AI processing), and there are a variety of helper threads for audio and stuff, but only one main sim thread.
Edit: and yes, the per-cycle sim time for 53,000 non-cold-storage units is a significant ms-budget-buster. It's got to check a certain number of things every cycle, and at that magnitude it adds up. There is still some render lag depending on the circumstances.