There are ways to toggle hyperthreading on and off so you can benchmark handbrake under both conditions. Of course, if handbrake can only use 4 threads, it won't matter if you have 8 logical cores..
As for cpuload, has it ever occurred to you that those programs don't have access to the necessary data to give a proper estimate? (
This site claims that while SPARC and POWER CPUs have "peephole registers" for this purpose while intel CPUs do not.)
From what I understand of the intel core it can execute four instructions per clock cycle, provided that it isn't starved of data, and the instructions are perfectly matched to the resources available in the core-- e.g. two integer and two floating point operations. By letting two threads share the core, it's more likely that this theoretical performance limit can be attained.