Oilskins?
 

Is there a mod to convert to oilskins as my men up top just wear there uniforms in the foulest weather with no protection,rather detracts from realism

Just submerge your boat and re-surface... problem fixed.
(As long as you are using Ubisoft's 1.4b patch that is...)

I have found this too - I have saved a game during a patrol in bad weather and the crew are wearing the Oil Skins. But if I save the game and later reload, the crew are back on watch in normal uniforms - most annoying! I don't know if this has a bad effect on the crew members morale level. But If I quickly rotate the crew on watch in and out of the boat they come back up in the proper rain gear :up:

just drag them down into the crew compartment and then drag them back up.