I've seen both. Have a game where its slow in any system, even one with no mines. The buttons to accelerate the game do nothing for example, because it's already going at less then 1x speed.
Now in that same game if you go into a system that has a thousand mines, it turns into a slideshow. All the ships won't even show up on screen, its so bad.
How do you know it's mine-related then?
Well, it's running just fine until the Vasari AI's get Ruiners. When (if) I wipe that player out and manage to clear the mines, some of the speed (but not all) comes back. Pre-Entrenchment I could play on the biggest maps and not have slowdown even at the endgame when the fleets are gigantic.
My guess is just that mines are treated as units. In the past, a 2000 supply fleet was likely less then 400 units, and there would only be a few of those on even the biggest map. One Vasari minefield is anywhere from 400-1000 units, and they put them EVERYWHERE.
I'm currently doing a bit of learning on how to mod Sins so I can mod out the mines entirely. When I manage to do it, I'll know pretty fast if the slowdown is mine related or not.