Rereading Buggy's introductory arc, they refer to the devil fruits as "gifts from the sea god" or something...

Here's my hypothetical explanation:

Devil fruits grow deep under the oceans. When they mature, they float up to the surface, where pirates find them. The specific origins of the fruits before they reach the surface is unknown, hence why they are able to scatter around the world, and also justifies how so little is known about them that many people consider them as nothing more than a myth.

Their connection to the sea is strong. They originate from the sea, and the ones who eat the fruit will one day return to the depths. This is how the cycle is established. This could also suggest that, even though no two devil powers exist in the world, a person could obtain a previously-accessed power if the original owner drowns in the ocean.