The scale is somewhat arbitrary, and it is adaptive. That is, it's automatically scaled in an attempt to remain as useful as possible, given the image and its current adjustments. If you create an image in Photoshop that has a perfectly even distribution of colour or grey tones (let's say a 256-pixel image with one pixel each of every shade of grey from 0,0,0 to 255,255,255), you'll get a block histogram with every tone "maxed out". Edit a few pixels, and the whole histogram drops to show you the variation in distribution.

Ultimately, you are interested in "none", "some" and "many", and beyond that you don't care at all. Clipping in the vertical scale just means "lots of pixels are at this value", and if it happens anywhere other than at/near black and white, it's essentially meaningless to you. If you photograph a subject in front of an evenly-lit mid-grey background, expect a whole big bunch of mid-grey pixels; it matters not a whit whether there are 8 million or 9 million of them unless and until things that aren't supposed to look like a mid-grey background are indistinguishable from the mid-grey background when you look at the image. You're probably much more interested in the pixels that aren't the dominant tone, and if the display is scaled to fit the dominant tone, you might not see them.