When the camera goes to the inside of the crate, Shaggy and Scooby-Doo are in their normal attire, but when they leap out, they have their scuba suits back on.
After Scooby and Shaggy, wearing scuba diving suits, are shot out of the air lock into the lake, Daphne, Fred, and Velma follow them riding in a crate in an attempt to save them. They are only shown coming out of the pipe into the neighboring river, but there is nearly no way they could have made it across the lake and into the underwater pipe without scuba diving suits. They would've likely ran out of breath, and even if they could hold their breath for that long, the crate would've sunk (or floated to the top) before being pulled into the vacuum of the pipe. However, as they were shown completely dry when emerging from the pipe, it is likely the animators forgot about the pipe being completely underwater, or purposely ignored this in order to quickly transport the rest of the gang to the river to explain the crime.