Yes, but it's hard to tell sometimes. Did the ship you sank explode, or just sink? If it exploded then you probably used up all its hitpoints and flooding didn't matter. If it just sank real fast then it definitely flooded. In the stock game they never sink until the hitpoints are gone, then they explode. If they sink without exploding, then flooding is working.
On the other hand I've had ships take so long that I put another torpedo into them just to make sure. Would they have eventually gone down or not? I'll never know. My patience isn't unlimited.
