The ships may well have been exceptionally large - I can't remember the exact words, but in Akallabeth it says that Ar-Pharazon's 'flagship' was huge - being as big as a castle seems to stick in my mind. So, there could have been hundreds just on one ship. A BD-er who is less lazy might like to look it up.
The Endeavour? Small? It didn't seem that way when I went on it (the replica I hasten to add, I am not over 200 years old)! I think they crammed something like at least 200 men on board. It was converted from a coal carrying boat. There's a nautical term for these which I've forgotten, and it's going to annoy me now. These were designed to be shallow bottomed. That's probably why they chose to convert a ship, if it was intended to go into shallower waters.