How did "shortly" acquire its seemingly illogical meaning?

"Short" and "brief" are synonyms; an event that is "short" or "brief" occurs for a short period of time. Yet "shortly" and "briefly" are not synonyms; an event that shall occur "shortly" shall occur in a short time, while an event that shall occur briefly shall occur for a brief period of time.

The meaning of "briefly" follows the normal rule for forming adverbs from adjectives, but the meaning of "shortly" does not. That is:

• If I stare lecherously, that means my staring is lecherous
• If I devour greedily, that means my devouring is greedy
• If a building collapses spectacularly, that means its collapsing is spectacular
• If I will visit briefly, that means my visiting will be brief, BUT...
• If I will visit shortly, that does NOT mean my visiting will be short, which breaks the pattern

How, and when, did this puzzling state of affairs come to be? It's not even as though English lacks other words to express the meaning "shortly" has - we have the perfectly good words "soon" and "imminently", after all - so how and why did people ever even begin to use "shortly" in this seemingly illogical manner?

This meaning of "shortly" goes way back, it existed in Old English. The earliest dated attestation in the OED is from 1325, but there are older OE examples without dates.

At that time it could also be used to mean briefly, but this meaning has become rare after Middle English.

I don't see any particular reason why "for a short time" should inherently be preferred over "in a short time" as the meaning. It's pretty arbitrary which one eventually took over, and things like this happen organically -- it would be difficult to pinpoint a reason.

Adverbs don't always follow the pattern you describe. Another example of a deviation is "happily": if I will do something happily, it means I will be happy to do it, not that I will do it in a happy manner.