How else would you tell the difference, some kind of evil gotee?

The hoodie is already used to typecast criminals, drug dealers in rough neighborhoods, etc. It's also a sign of relative youth (<40 years old). Dark places are an uninventive way to say they're doing something "bad". What's funny is that while they are depicted as being smart/dangerous, they're also depicted as being white and male, which is also a usual sterotype and conveniently forgets the proportion of extremely knowledgeable people of various origins and genders out there.

Images and ideas have entered the mythos over the years, I doubt there is a "source" but more of a collective myth which has grown and evolved with some sources in reality and some of reality fashioning themselves after the myth.

But also, I have just known lots of computer people that liked to work on their interests late into the night in a dark room.

You might say Cyberpunk styles are a source. https://en.wikipedia.org/wiki/Cyberpunk

I think it comes from recent popular media, like the Watch_Dogs games and the TV show Mr. Robot. Hoodies are a way to prevent people from seeing or identifying you, so media people use it as a visual shorthand for "this person wishes to conceal their identity". Back in the 90s, hackers were all cybergoth ravers; this image is more in line with the $CURRENT_YEAR zeitgeist in which pervasive surveillance is a top issue.

They're symbolic, not realistic. The only reason they wear a black hoodie is because a striped black and white shirt with a black masquarade mask is because it's too silly.