The born counter bug is now fixed. You will see it in 2.42.9 or 2.42.8c, whichever comes first.
The accumulation of mutation history can impact long run evo sims. You might want to save the sim without mutation history and then re-load it and see if that has a speed impact.
Also, as bot genomes grow in length, or mutate to non-zero values, it takes longer to execute each bot. A sim runs fastest when it full of bots with short, 0 valued genomes. You should expect null evo sims to slow down over time.
There are a number of perf improvements in the recent buddy drops. Nothing earth shattering, but every bit helps and I am continuing to profile and make improvements for 2.42.9.