The short answer is, they weren't. The Cacafuego was properly named Nuestra Señora de la Concepción, "Our Lady of the Immaculate Conception;" the scatalogical nickname is just a nickname. I don't know as much about Spanish naming conventions in the 16th century as I do British, but my strong gut feeling is that there were tons of ships named "Nuestra Señora ...", as it's a fairly generic moniker. (Columbus' flagship was La Santa María de la Inmaculada Concepción.)

So the Spanish sailors aboard the ship may have chosen the nickname to distinguish their ship from the other various Our Ladys, or may have chosen it for its warlike qualities -- we simply don't know, or at least I don't know of, and haven't found, an English language source that's definitive on the answer. (My Spanish is no bueno.)

I do know that in the Royal Navy, nicknames (some in Cockney slang) were a way of showing affection for a ship, and they persist. Churchill was rebuffed by George VI for wanting to name a ship after the Pitts (Elder and Younger) -- George VI, the former Prince Albert, had served in the Royal Navy and rejected the suggestion immediately due to the obvious nickname. Churchill grumbled that the thought was unfit for the royal mind.

Incidentally, of course, in his retelling of the fight between El Gamo and *HMS Speedy," Patrick O'Brian renames Gamo to Cacafuego, as the foil to Jack Aubrey's Sophie.