Aurora is using older Visual Basic code and can only use one CPU and the RAM you have is hardly relevant unless you have an older machine. This would explain the low CPU load.
If you don't have an SSD disk this might also be a minor issue since the game basically saves everything to the database on the disk all the time.
You can have a huge civilian fleet or your NPRs might have, these will make sure slowdowns do happen. Don't subsidise the civilians too much or you might get too much lag from a that fleet. As far as I understand the code is not optimized in regards to civilians scraping older models. In the new 6.4 version Steve has mentioned that some of this will be fixed and that civilians will be able to build even larger ships as well to mitigate this problem. Although it would not solve your problem...
Those are the thing I could think of aside from what was mentioned above.