The hatch was pretty small and the water was quite deep. It wouldn't surprise me if the hatch fluttered down hundreds of yards away from the capsule. In all that time, it quite likely would've been covered with sediment, making it very difficult to locate. The fact that they found the capsule itself is remarkable.

You're right, the best evidence shows that Grissom didn't blow the hatch. Ironically, that might've contributed to his death in the Apollo 1 fire. The Block 1 Apollo capsules didn't have explosive hatches. Instead, the hatch opened to the inside and sealed against the frame. When the fire broke out, pressure inside the capsule quickly forced the hatch so tight against the frame that it was impossible to open.