So why are overhead kicks permitted in a crowded box and why are keepers allowed to punch near and over people's head(often catching people as they do) etc?
For the same reason many other dangerous tackles are often not given as fouls if no contact is made, when contact is made, refs tend not to overlook it and Nani made some serious contact.
But again, a high foot and contact isn't necessarily powerful or extremely dangerous, Nani's contact was off the ground, he was moving at speed and his entire weight + speed was all put straight into Arbeloa, an overhead kick doesn't have the same criteria, there is FAR less power, the weight is moving down, its very rare for a player to be running when he does an overhead kick.
I genuinely don't know if people are being intentionally obtuse to really basic physics/common sense or if people really can't understand it. The power a human can generate with a standing kick, and running, getting up some serious speed and jumping at something is completely different, the direction/action of the kick is also important. Nani hit him dead on, with no where for his weight to go, if Nani had his leg out to his side and jumped 1 metre to the right, he'd still of kicked/caught Arbeloa, but it would have spun Nani around like crazy and little of the power would have gone into Arbeloa.
The basically most dangerous thing you can do is jump into a tackle with your leg out infront with all your weight following, its the least in control and the most likely to do damage.
Overhead kicks are usually given as fouls when contact is made, but you rarely see anyone injured seriously, though there was one only last weekend, it just highlights the point, they are dangerous and should probably be carded more often than they are.