Ah, maybe it's not your hard drive access, then.
Usually when your mouse appears to lag, it's just because you're experiencing a low frame rate. Hegemony doesn't use any fancy hardware cursors, so when you're experiencing low frame rates, it also affects your cursor. The easiest way to measure your frame rate is to install a program that displays a frame rate counter, like Fraps.
However, sometimes lag is the result of the "flip queue" (or "pre-rendered frames", as nVidia calls it). This happens when your CPU is much faster than your GPU, and can queue up several frames, which makes it appear as though you have a high frame rate, but by the time the frames are drawn, they're old.
We fixed this for most users years ago by simply limiting the FPS to 60, but you can try lowering the FPS cap to see if that helps. We don't have a setting for this in-game, but in the SafeSettings.xml file you'll see a setting called "FpsLimit" which you can play with.
Alternatively, you can install a program called "RadeonPro", which lets you modify how big your flip queue is. Turning it down to 0 should reduce lag. NB: I've never tried this program.