Yes the damage models have been changed in GW. Now ships have more of a tendency to sink from flooding rather than you just exceeding their max hit points. This means that you can completely destroy a compartment but the ship will still not go down. Spread you shots around.
This was intended to intruduce a bit of uncertanty like the real skippers had to face. No more insta sinking
Your deck gun is also less effective so aim for the waterline.
Generally I will wait about 2 hours max. If it hasnt one down by then I plug it again.
However, it can take much longer than that for a ship to go down.