As far as I know all ships will re spawn and if you sink the same ship later you may not get credit for the second sinking. For merchants if you're in the same area and sink a second Maru that is on the same course as the first, no credit. This doesn't happen very often.
As far as abilities go, the only solution I know of is to fire the guys and hire someone that has no abilities. Make sure you keep the important ones.
This game is pretty much for the PTO so no raiding Germany or America.
For a U Boat career I would suggest installing the Operation Monsoon mod.
Welcome to the boat mate.
Magic