Hmm. I doubt it would go from "fine" to "freezing" due to just a few carriers and fighters. Also, if it's running fine in the command screen (tab screen in combat), that's an indicator it's probably not a problem with the number of things in combat, since it just renders more things in that mode - it's "regular combat PLUS the map UI on top of it". So it really doesn't seem like it's related to having some more ships/fighters deployed.
Are there any errors under System or Application in the windows event viewer? Do you have any other software running? In particular, MSI Afterburner or anything similar, or an anti-virus. If so, I'd try turning these off. I'd also try running the game in admin mode, and in compatibility mode for Windows 7 or XP.
Might also be worth looking at assorted system resource use - RAM, CPU - when it freezes. And, again, making sure that your graphics drivers are up-to-date.
I'd also suggest rebooting, if you haven't already. It kind of sounds like something on your system changed between when it was running well and now, and if that's the case, a reboot might fix it.