It is quite possible to miss the relatively small water columns from .50 cal rounds. If the small craft was upwind, hearing either a hail or the firing of light arms could go unheard.
Depending upon the lighting and sea surface, the latter could also be unseen.
Presumably though, the ship would have sounded its siren or ship's whistle - either of which can be heard for miles upwind in anything short of a gale.
It is not beyond possibility that the guys in the boat could have been completely oblivious, or they could have been playing at jihad.
In any event, speaking as ex-navy and given what happened to USS Cole I think that the crew of Rappahannock made the right decision to fire on the oncoming small craft - especially given that Rappahannock is an oiler & would not have survived an explosion the size of which USS Cole suffered.
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