While I was in a cube I actually locked my running laptop within a large metal filing cabinet and used it for RDC with no problems. The volume of air within the cabinet was sufficient enough that the air could circulate and be cooled by the metal exterior. Of course I was not running my CPU and disks at 100% for long periods of time.
If you boss is willing, why not purchase a small 3 U locking rack and put that in your cube. You could then use 1 U for your laptop and the rest of misc. storage. Sweet!