i never have problems with slowdowns/freezes unless im playing mods, or this one map i have where someone re-created the entire universe from the game freelancer...
58 planets, 1155 gravity wells (its a massive map, lots of work went into it, but it was designed poorly... certain space stations in the game Freelancer are represented as GWs in their own right... nebulas in Freelancer are massive, so in this map they are represented with multiple UCGW's... but meh)
after i send out enough scouts, and i have explored about 60-70%, have most if not all AI slots filled, and have expanded into one or more other systems, then the game starts to lag for me
my comp is a Dell XPS 1730 Laptop with dual Intel Core 2 Duo T9300's at 2.50 GHz a piece, 4 GB DDR2 (i think), dual Ge-Force 8800M GTX Graphics Cards at with PhysX and SLi Tech 512 Mb a piece, 17" High Def Monitor with 1920x1200 resolution, running Vista 32-bit OS and DirectX 10.0
so yeah, unless i have the settings on high, and am playing a mod or that large Freelancer map, the only problem i ever have is that the first time i start it up after a long tme not playing it, it takes ages to load up, but i doubt thats to do with the program and more with the fact ill have other stuff going on (both my 200 Gb hard drives are pretty full atm, so im feeling sorry for my laptop...)
there could also be problems with your registry files, clogging up your computer... download CCleaner (google) and run it, it really boosts performance and will often clear GIGAbytes of scrap data off your hard drive. also running a virus check and ad-ware/spy-ware cleaner on your comp to clean away the cob-webs every once in a while is a great way to speed up your comp...
but yeah, the game isnt broken or buggy... 9 times out of 10, its your computer, not the game... make sure you are all up to date with all your drivers, and that you havent got a virus somewhere (or even your own virus checker/firewall) slowing your down. if you still have problems, contact support@stardock.com and get their help
Good Luck