That's why perfume was invented. They had to have something to cover up the stench. Even the upper classes didn't bathe that regularly, though they did so more than the commoners. To the superstitious, bathing was thought to steal the soul, so they rarely bathed. The upper classes did so infrequently because they thought you could 'catch your death' of cold.
If Elizabeth can seduce Jack looking (and probably smelling) the way she did, pretty much like a wreck, then i dont have any trouble believing that Jack somehow manages to smell pleasant. i would imagine that Jack smells most strongly of alcohol, which can actually be a nice smell sometimes.
Pirateslifefo, are you anti-Jack? Or did you get to kiss him and therefore know first hand about the smell factor? 😉