I'm only guessing but it reminds me of what are called petechial hemorrhages in humans, which have many different causes, one of which is a vitamin C
deficiency. We've mused about Vitamin C's role in healing a snake's skin, so you might try a supplement (one for reptiles!) that contains it, just to see?
My first thought was that your snake bumped into a branch, but from your description, it does appear to be a blood-flow issue...could also be genetic. It
wouldn't hurt to ask a vet but I'd faint if they had ever dealt with this complaint before. This might even be common, but on darker snakes no one sees?
Reading that link your right, sounds like what im describing. Its really odd, its so clean too so I cant find anything that got under the scales etc...plus I dont use anything but craft paper Substrate and i clean like a nut.