There is very easy way for you to confirm whether it is caused by custom AI. Change mission to use retail AI profile, in ai.tbl delete everything after $patience in each class.
Edit: I Just realized there is indeed one factor that may cause slowdowns; AI Fire Delay Scale. If you have weak CPU which cannot handle significant increase in weapons effects on-screen, you might have issues. This would only be an issue if you use custom AI on capital ships or any weapon with really high rate of fire. However, The E who is also a BP staffer, has fairly weak (by modern standards) 1.5GHz Core 2 Duo does not receive heavy slowdowns in WiH which is largely unoptimized in terms of model and texture efficiency, so performance in plain mediavps is even better.