First, they swabbed the whole deck not just the poop deck. The focus on the poopdeck is probably modern because it sounds interesting and sticks more in the mind.

Supposedly they swabbed the decks in part because salt water prevents wood rotting (versus fresh water from rain storms which promotes rotting), in part because it’s a wooden ship with gunpowder loose which is a fire risk (so best to sweep it away and keep areas damp), and in part because it kept the crew occupied.