Many elderly characters are depicted as short/small (even, I would go so far as to say, in any sort of media). Take WW-Link's Grandma, Oshus, that old Goron in MM to an extent...
I can see where you're getting your argument from, given that there are counterexamples in any race except the Sheikah. However, it is a common trend, and I think it's artistically exaggerated in Zelda just to emphasize that aspect of their character.
Not only does it build on the character itself, but it creates a contrast that relates the character to its context. Impaz's smallness in TP emphasized how empty the Hidden Village was, and how frail the legend of the sky messenger was. Impa's height in SS is mostly used to contrast the two states of the character. Functionally, it helps hide the fact that they're the same character until it's revealed in the narrative. It also, as the above posters have said, helps to make the vast passage of time believable. If you study video games, you'll find that many elements aim to support each other - create a redundancy - be it with music and sound, art style, colors, field layout, gameplay, whatever. Impa is radically different in the two times to reinforce that the two times are radically different.