Mainly, sins only use one core... a second core is only used for load the texture...

A trick is possible but it is not a simple one... myself, i have two quad core Xeon at 2.66 ghz... Using a hardware virtual machine ( processor need to have virtualization ( intel VT-x or AMD-V) , and bios need to be able to enable it for the intel VT-X ( AMD-V is always enable ))... using VMware ESX Server edition allow me to create a virtual processor with 10 ghz frequency... only limitation is 4 processor by Virtual machine ( multicore processor are only one processor )...

A other method that i use now is using linux with a custom kernel... called KVM kernel along with QEMU ( who allow me to emulate a lot of different processor type )... these method is good but you need to be able to compile your own kernel and the needed modules ( called driver in the windows world )...

Almost forget, in both case, online game don't work...

For the future, i don't think that Stardock will make the engine multi core and/or 64 bits... reason is simple : need to rewrite a lot of the code... more, Stardock is not the devs of the iron engine, Ironclad are the devs of the engine... but it is possible that in a few years, if a Sins2 is created, that the new engine will support more modern technic...

in the later stages of the game, especially with multiple star systems and AI opponents, the game becomes very choppy using anything other than the standard 1x game update speed.

Put the AI on hard or unfair... AI, in place of stock huge fleet in some place, will attack... this will reduce the number of object in the game... maybe you will regret that 1/2 speed don't exist when you need to fight and make a lot of micromanagment on a huge map...

Now, for entrenchment itself, it is a Beta, not yet optimized... speed will be better in the final version ( i hope )...

would the multi core program written for sup com work with sins?

By which he means, the limitation is inherint in the programming of Sins -- trying to change it with an outside program should be impossible.  I'm not an expert, but if someone found a way to force it to use multiple cores... well, a program that can do that in a 'generic' sense (e. g. written for SupCom, but works with Sins and therefore probably most programs) would make a person between millions and billions.  That kind of programming... well, it's not possible, really.  You'd have to re-write their code from scratch, on the fly... 

Something else I should point out:  changing a program to use multiple cores is a huge task, simply because for years, programming has been based in a very linear design...  using multiple cores means you need to parallellize your code, and we just don't have the 'experience' to do so very much yet.