I'd have thought it's one of those phrases you use when you don't want to offend. Like saying "Naff off", instead of "F*ck off", or "For crying out loud" instead of "For Christ's sake" or "F*cking hell". In which case it would stand in for "Sh*t!"

I went through after I'd written this and put in the asterisks, in case there's a search engine somewhere that might freak if I didn't. I can't imagine pirates would worry much about that kind of thing, but I think it probably started life as a literary expression anyway.