They don't affect each other. The slowdown you're experiencing is a combination of a few things.
1) Your civilian companies get ridiculously huge and operate possibly hundreds of ships, all of which must be updated every increment.
2) Any non-player races are growing, exploring, and possibly fighting each other. If an NPR needs a lower time interval due to a battle, that's what you're stuck with, whether you're involved in the battle or not.
3) Those NPR's also have civilian ships just like you do in #1.