Yep, 3dmark is pretty heavily influenced by the number of cores in the CPU. The benchmark is pretty close to saying "well, 4 2.5 Ghz Cores = a 10 ghz CPU", which we know is not realistic.
In a perfect world, where programmers actually decided to balance a large multi-threaded system, yes... it would have an impact. Unfortunately, there are few games and programs out there which utilize multiple cores. Even if they do, usually one core does most of the work, and maybe one other core is used for offloading the sound engine or other game subsystem. This does help a bit, but it is far off from 3dMark predictions.
3dMark is nothing more than an E-Peen measuring tape, and has only vague correlations to real world performance.