Because "higher" is scalable (high, higher, highest). So is "low" (low, lower, lowest").
"up" and "down" are not scalable. The suffix "er" on "upper" and "downer" does not make them comparatives. In the case of the drug slang "upper" and "downer", it's an agentive suffix. Something that brings you up or brings you down.
"Upper" as an adjective means above or on top. "Lower" as an adjective means below or on the bottom. Consider bunk beds. There is a lower bunk (the one on the bottom) and an upper bunk (the one on the top). Likewise, the 1st and 2nd storeys of a house are the lower floor and the upper floor respectively. And we have lower and upper teeth. In other words, when there are only two choices, rather than degrees of "upness" or "downness", the two choices are called lower and upper.
There is not always symmetry in word usage. Our up-and-down words present other counterexamples: Consider lower the bridge. Now, if you put it up again, what did you do? You raised it—you didn't "higher" (or "upper") it. And back to drug slang: you get high but you don't "get low"—you come down.
Anyway, I agree it's peculiar. But that's how English goes. I'm not an etymologist, so I'll leave it at that.