No, knees to the head does not necessarily benefit grapplers more. It can in certain situations, but it takes away the strategies that people find boring or against the spirit of the sport.
What it does is allows there to be less artificial positions. An example of that is indeed, a grappler being in north south position and landing knees.
But also someone sprawled on another guy, and landing knees, instead of having to either just stand up or risk spinning to their side (which in turn only opens up punches that are weaker than a knee to a head).
Or of course the thing where guys dive for a leg, put their knees on the ground, and keep their head low. Wrestlers who are "chain wrestling" against the cage are doing so knowing that there is no striking repercussion, because you can't knee them at all while they're down there, and you obviously are not allowed to hit to the back of the head.
So even if you stop their takedown, you are still forced to engage in grappling, since it's the only way to get out of there (wrestle and spin from the cage or threaten with some type of choke and hope they let go).
Asian MMA has knees to the head of a grounded opponent, and those promotions typically do not suffer much from lay and pray.