I always assumed that Velma's sexuality, though subdued, was not constrained by our limited concepts of gender.
Being a lesbian isn't offensive. Making blanket assumptions about someone's sexuality based on superficial characteristics is offensive. Just as it's offensive to apply unrelated stereotypes onto people because of their sexual orientation. I don't know that we need to take James Gunn too seriously on this subject. IIRC, his original version of Scooby-Doo was going to be an R-rated piss-take on the franchise to appeal to its adult fans that watch it ironically. It was undoubtedly going to revel in all of the assumed fan cliches, including Shaggy being an outright pothead and all the Fred/Daphne banging.
That largely depends on the intent of the one making the assumptions. In some cases, it is for awful reasons and generally done by bigoted people because they don't like gay people and hate those characteristics. In other cases, it's queer people sensing some similarity and latching onto a character. This was more common in the past since LGBTQ representation was lacking until very recently and generally very negative. It's done out of affection and the need to identify with someone on a show. Velma's association with being a lesbian started out as mostly tongue in cheek (like Shaggy being a pothead), but evolved into something positive as queer fans adopted her and I don't think it's right to take that away from them. That's why there has been some attempts to make her officially a lesbian, it expands her as a character, honors the original inspiration and her achievements, and she would be positive representation. And there's nothing offensive any of that.