Initially reported by /u/wh1tepointer on Reddit.
Using ScriptHawk in DK64, you can turn on "Object Model 1" in the options, which displays all of the actors in the scene:

In Bizhawk versions 2.8 and earlier, this works as expected, the actor list displays and performance is unaffected:

In Bizhawk 2.9 and later, this is broken. The list of actors does not display, and the performance also slows to a crawl - I'm talking dropping from 60fps down below 20fps and even sometimes dipping into single digits:

I did notice you're using the bit library in some places but never import the shim, so maybe that's related.