This is bang on, you can't count the hyperthreads as double the performance, typically they are actually in practice only going to bring 15-30% if the job works well with it and their use will double the latency. Failing to account for loss in clockspeed as the core utilisation climbs is another way its not linear and in modern software for the desktop its really something to pay careful attention to.

It should be possible from the information you can get on a CPU from the OS to better estimate utilisation involving at the very least these two factors. It becomes a bit more tricky to start to account for significantly going past the cache or available memory bandwidth and the potential drop in performance to existing threads that occurs from the increased pipeline stalls. But it can definitely be done better than it is currently.