Thanks for taking an interest chaps, it's got me baffled. Can't get over to the boat for a day or two, when I intend to do more checks.
To answer the questions.
Only the starter battery is fitted, it is earthed to the engine.
It was isolated at the time. (but not the earth)
There's no bow thruster.
I've since spotted a thin red wire connecting the starter battery directly to the coil of a small relay, haven't found out what this does yet, but it appears to head towards some engine bay extractor fans, via various "devices" which appear to have been tacked on over time. (hence the rewire), one of the fans is suspiciously close to where the short took place, but I can't see any damage to any wires, or any exposed terminals.
I'll let you know if I find anything, but any ideas would be useful.
Steve