How big is the hole?
Trunks are big and the bottom of the hole is level with the deck. Usually they have a "top hat" fitting screwed to the transom or a bit of plastic pipe that sticks out the back gooped in through the bore of the hole. All trunks usually have a rope with a cleat on the transom (usually a jam cleat) to raise it (althoug hsome like mine are led back to the helm position, so you might not find a cleat, but it's highly likely if it is a trunk hole). If you can see a cleat or the old mounting holes - it's probably for a trunk. Lots of places will sell you replacement trunks to fit to it. (Hypalon goo & a tie wrap will work nicely)
If the boat has a hollow floor, I think I'm safe in saying Seariders are the only ones with the flooding hull. Most ribs have a small drain bung which is uslually almost at the bottom of the transom's V. If this is your hole - bung it!
Better still - post a pic & remove all doubt form the answers!