Hi,
I've got a massive slowdown problem, too. There's a simple way to rule out your guess that it's a memory problem: Reduce the graphics to minimum. You will notice that the game uses around 550MiB in that case, but still suffers from the extreme slowdowns!
Someone mentioned that trade ports would cause it. I think it's multiple issues, but the slowdown typically becomes much more dramatic after building a few of those super guns like deliverance engine.
The real problem of the game is (aside from the numerous unfixed bugs) that it only maxes out a single core while graphics card and the other cores are idle, even if the game is set to maximum graphics settings (it's using around 1.4 MiB in that case).
It's also not the computer enemies that slow things down. There's an easy test for this: Finish a medium-large map by destroying all your enemies. The slowdown won't go away, although there's no combats going nor any fleets moving (except trade drones).
For me, the slowdown is most bad while playing advent although they don't even have resource ships, only trade drones!
I do wonder wether fighters/bombers are also causing constant CPU load although they are not required to do anything when there's no hostile ship around. At least it felt like a slight relief from that slowdown after docking all ships on their planet's hangars. However, the game still was somewhere around 3 real time seconds for one game second afterwards.
Screet