Scooby Doo has always been a wholesome, enjoyable, and predictable cartoon (the bad guy is always second guy you see!). Despite the family friendly nature of the show, there have always been some subtext that bother the older crows.
The sexual tension between Freddy and Daphne? The fact that the every arrest was just for scaring people? These aren't even the worst offenders.
The biggest is that Shaggy is obviously a stoner, something the voice of the character never realized.
The rumors of Shaggy's recreational uses with marijuana surfaced thanks to his constant hunger, his talking dog, and his crazy, paranoid antics. However, the voice of the character, Casey Kasem, said "there wasn't anything like that at all" when asked about if he had every observed the subtext. He said "guess it's because, I don't know, it was a wholesome show from beginning to end." The first time he ever thought of that viewpoint was when the interviewer brought it up.
The recent Scooby-Doo films had several shots that referred to Shaggy using the drug, but many of them did not make it into the final cut. The character that played Shaggy in the films also didn't believe Shaggy smoked weed. "He just seems like that. He acts a little goofy and high, he's lovable and scared—and just happens to have the munchies."