Learn English – What are antonym-like prefixes to the Greek “crypto”

I don't think that it's the same prefix as much as it is the remnant of a number of different grammaticalised pre-fixings. Most of them seem to have happened during the period when then curious admixture of French, Viking Danish, Anglo-Saxon and a sprinkling of Gaelic were distilling themselves down into the various dialects of Middle English. The spelling's kind of arbitrary, but a is the letter we tend to use when a word starts with a schwa that's flatter than we'd represent with a short e.

English was essentially an unwritten language during that period (and the population essentially illiterate), so it could be a time of great flux. A lot of words were repartitioned. All one became alone, the n sound migrated from the ends of words like mine and thine to become the initial (and previously non-existent) consonant of words (especially eke names -- thine eke name also became thy nickname) and so on.

As with a lot of what happened during this period, what we have now in the language is mostly what was present in and around London when the orthography was fixed by printing. Many of the a- words that one recognises as quaint regionalisms today (like a-hunting) were standard in dialects that did not, themselves, have the good fortune to become the standard themselves.

As for new words, well, printing (and general literacy) sort of put a stop to arbitrary movement of word boundaries. A question was posted here earlier asking about the meaning of "grab a hold", and it didn't take long for somebody to reply that the phrase was actually "grab ahold" (something my spell checker has decided is a problem). I would bet that "grab a hold" or "take a hold" (hold being synonymous with handle, as preserved in hand-hold) was the original phrase. They sound the same, and if you hear a hold often enough without seeing it written down, there's no real reason why you might not think of them as a single word.

The word occurs in one of Stevenson's essays. He is reflecting on the ways in which a writer may choose to approach the subject of his writing:

"There is a vast deal in life and letters both which is not immoral, but simply a-moral; which either does not regard the human will at all, or deals with it in obvious and healthy relations; where the interest turns, not upon what a man shall choose to do, but on how he manages to do it; not on the passionate slips and hesitations of the conscience, but on the problems of the body and of the practical intelligence, in clean, open-air adventure, the shock of arms or the diplomacy of life".

Today, 'amoral' often has connotations of being unable to tell right from wrong, but this is clearly not what Stevenson had in mind. He was simply drawing a distinction between those actions that have an obvious moral dimension and those that either lack this dimension or where (speaking as a writer) this dimension is of secondary importance.

So the meaning of a word is liable to change with time, or the word acquires new senses; and as John Lawler has pointed out, a word borrowed from another language cannot be relied on to mean what it meant in its parent language, nor can its meaning necessarily be derived from etymological analysis. The latter is at best a guide to the meaning, not an infallible marker of it.