Hello Ross,
Who did you get to check the records in the Fifth Register of Seamen? Did they check BT 382/326 - that is where his records should be if they have survived. Not all have so you may just be unlucky? You say he was invalided out of the MN, do you know when this was? If he continued to serve after the war his records may be lurking in the second series held in BT 382/2193 - although I suspect he was invalided out before the end of the war - am I correct?
With regard to your other question re crew lists, when a vessel was lost at sea, its official logbook, which includes the crew agreement, would have been lost with the vessel. In these circumstances the owners would submit the copy of the crew list that had been retained on shore to the RGSS. These lists were then used for registration of the deaths of the crew. So to answer your question, yes, there should be an official logbook held at Kew in BT 381. You can check if there is an official logbook by searching online using the ship's official number. Need the name of the ship to start with?
Regards
Hugh