In Ghosts of Saltmarsh, stats for Longships and Keelboats show that they are close to the same size if you measure length and width (70ft x 20ft and 60ft x 20ft, respectively), but are very different in terms of capacity. A keelboat can carry a total of 7 creatures and .5 tons of cargo, while the longship can carry 140 creatures and 10 tons of cargo.
Is height the main difference between the two ships? These stats lead me to believe there's a belowdecks for the longship that doesn't exist on a keelboat, however it's worth noting that other ships with multiple decks have that spelled out, whereas the longship does not.