"Yes"
It's the only bottleneck on the system. It's not really slowing the game performance, it's slowing down the loading.
If you disable Vsync, you will probably hit 100FPS easily, but the system will have a quick pause while it uses the HD.
You are over thinking the issue, though. 1 FPS is normal and the measuring tool may not even be that accurate. It's most likely the measuring tool stops responding when the disk is in use.