"Like" versus "not unlike"

"Not unlike" is slightly different than saying "like" much like saying "I love apples" is not the same thing as saying "I don't hate apples." It emphasizes a different degree of likeness. "Not unlike" just means that there exist similarities while "like" means they are similar.

Two objects can have similarities but not be similar, such as an apple and an orange are both fruits, so I could say "An apple is not unlike an orange in that they are both fruits." However to call an apple similar to an orange is perhaps a bit much.

Also consider that the meaning of "like" has many meanings, and is therefore a little ambiguous. So I notice a tendency to prefer "not unlike" in books in order to make the meaning clear that you mean to say that two things have similarities.

how did this double negative come to be?

About 100,000 years ago, during a conversation about antelope, Ug grunted twice to Og, and lo, litotes was invented.

Which is to say that it will have arisen naturally as part of the development of spoken human language at a time before writing had been invented, so no one will really know exactly how it came to be. It just obviously fills a subtle linguistic need to communicate the degree to which a verb applies to a noun.

Disclaimer: my knowledge of these things is not entirely unlike Ug's.