It's impossible for anybody to say for certain, but it is definitely a distinct possibility. Artists' interpretations of the Colossus seem to swing both ways, but most commonly the assumption is that it did indeed have junk. And everybody knows that if artists a thousand years after the fact thought so it must be true.

Anatomically correct sculpture was certainly a thing in ancient Greece (they had been putting dicks and balls on posts indicating road markers, called herms (or hermai), for centuries by the time the Colossus was built). These were considered sacred to Hermes (and commonly had a bust of his head on top), and were associated with his role as the god of travellers. On the other hand, the Colossus was meant to be Helios, not Hermes.

But it's important to note that the colossus was, most likely according to what details we do have, an iron frame with bronze plates (or brass, or I've read one source that said gold but let's be realistic here), attached to it, and attention to detail would have come second to 'what can we do with this without worrying about bits falling off'.

What I can say with a certain degree of certainty is that nobody was sailing underneath the Colossus at all, looking up at its junk or otherwise. That bit about it straddling the harbor is a cool mental picture, but complete bunk, it was a story told to travelers who spread it around because it sounded cool (most commonly attributed to an unnamed 14th century Italian). What information we have indicates that it stood upright on a large marble platform.