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.
It’s not “media people”, I can assure you that most modern street criminals wear hoodies. It’s a cheap and easy way to switch to “incognito mode” at will. In places like London and Manchester, most crime-related CCTV will feature hooded thugs. There have been arguments about forbidding hoodies in public areas and shopping malls all the way back to the ‘90s.
To be honest it’s as old as capes, we’ve just lost the cape.