If you look at the CSS box model spec, you\'ll observe the following:
The [margin] percentage is calculated with respect to the width
I realize the OP is asking why the CSS specification defines top/bottom margin percentages as a % of width (and not, as would be assumed, height), but I thought it might also be useful to post a potential solution.
Most modern browsers support vw and vh now which lets you specify margin numbers against the viewport width and viewport height.
100vw/100vh equals 100% width/100% height (respectively) if there's no scrollbar; if there is a scrollbar the viewport numbers don't account for this (while the % numbers do). Thankfully, nearly all browsers use scrollbar sizes of 17px (see here), so you can use css calc function to account for this. If you don't know whether a scrollbar will appear or not, then this solution will not work.
For example: Assuming no horizontal scrollbar, a top margin of 50% of height, could be defined as "margin-top: 50vh;". With a horizontal scrollbar, this could be defined as "margin-top: calc(0.5 * (100vh - 17px));" (remember that the minus and plus operators in calc require spaces on both sides!).