Maybe Vecko or someone else can confirm this, but if you have the crew at battle stations or silent running then they will not try to repair things. Or maybe it is just one or the other i'm not sure.
The second thing is damage, if you get nailed by a direct hit then you are pretty much done. I just started a new campaign with Wolves of Steel and during Baltic Operations I was attacked on the surface by a destroyer that sneaked up on me while I was busy trying to deck gun a merchant. I had to crash dive but luckily her shells only landed near my boat. Two members were injured and the boat was slightly damaged and I had 3 - 6% flooding in 3 compartment. The crew got the flooding under control and got it all pumped out while I was submerged. So they definitely work.
