You should probably pay off his debt before he leaves the ship. Once you do
he sells items really cheap while he's on the ship - so you can buy from
O'aka and sell to Barkeep and make a nice profit (I've heard Holy Waters are
the best item for this, even though High Potions are more expensive, since
you make a smaller loss on the buy/sell ratio of the Holy Waters).

Not paying off the debt before Chapter 3 (not 4) means you don't get the
completion percentage, so, yeah, you're stuffed as far as that's concerned.