James Gunn, who wrote both live-action Scooby-Doo movies from the early 2000s before going on to a much more high-profile career directing movies for Marvel and Warner Bros,, also commented on Twitter that Velma was “explicitly gay” in the script he wrote.
Mystery Incorporated confirms that the show always intended its Velma Dinkley was gay.
The studio (that would be Warner Bros. again) “kept watering it down” until all traces of that element of the character had been removed.
If you have spent any amount of time wondering about the sexual preferences of the Scooby-Doo gang, this information may be of use to you.