Tricky things they are...
I also noticed that normally only a single raft spawns after every sunk ship, but recently I decided to create a little surface battle with the mission editor, and I got this after a jap BB went under.
So something is obviously not right. As for them dissapearing...now that you mention it, I didn't see them after the battle calmed down, even though they should have been quite visible in the aftermath, yet only oil slicks and a few "not dissapeared" derelicts remained (curse the limited engine, could have been an awesome underwater ship cementary, especially since I palced them in shallow water).
It's possible that they are destroyed by the secondary explosions and that's why they sink, happened to me once, it could easily happen to them as well, since they are practicly right next to the fireworks.