1. How can I improve the boot speed?
Alt1: Go into the BIOS and disable the SAS ports. This will make the time from start to Windows boot dramatically faster.
Alt2: Install Windows on a SSD drive.
2. Hyper threading - would my system benefit by having this enabled.
Yes.
3. Regarding Windows Experience index: 6.8 > Graphics giving me the lowest scores (NVIDIA Quadro K600).
With a Quadro K600 that´s expected. Buying a new/better card may not be necessary depending on the applications you use.