It has been a while since I played, but I don't recall being able to repair damage at sea. Looking at my manual, it looks like all you can do is check the damage report with the "b" key. If you want to repair the damage then you have to go back to port. During your refitting in port all damage will be repaired.
I don't think this detracts from the gameplay and it is probably more realistic this way. In reality, a hit from a modern weapon is likely to sink the sub outright. So if the sub survives the hit then it would make sense that the damage would be so severe that it would require that repairs be made in port.
This is a great old game. Much better than any of the modern games, in my opinion. In this game my main priority is always the safety of my ship, so I rarely get hit. If I do get hit and receive damage I immediately head back to port to get it repaired. Limping home from a brush with death is part of the fun.
In case you don't have them, you can find all the manuals and maps for download here:
http://www.abandonia.com/en/games/48...rm+Rising.html