When it comes service assignment time, and if one is marginal for an assignment to aviation because, maybe, their class standing is relatively low or their ASTB (Aviation Selection Test Battery) scores were not that impressive; having a "resume" that indicates interest in aviation and aptitude may be a difference maker.
Quite frankly, getting a pilot slot is not nearly as competitive and difficult-to-get as it used to be. The long commitment causes some to shy away from it. Also, the many recent "horror stories" about how the Navy is raising the bar extremely high in the flight program, specifically to thin the ranks, is discouraging to some. Most of those who quit or wash out of flight school (oftentimes, before they have even touched the controls of an aircraft) are discharged from the Navy. The Navy waves their commissioning obligation and gives them an "honorable discharge". In other words, you become unemployed.
As far as having prior flying experience helping in the flight training program - it helps a bit - but not nearly as much as you might think. And, even with that, it only helps at the very beginning. After a couple weeks the advantage of having a private pilots license completely vanishes and natural aptitudes rule the day. An individual with no prior flying experience, but who has natural aptitudes, is going to do better than somebody with prior flying experience who does not possess those aptitudes.
As an appointee to the Naval Academy, I would concern myself much more with what you can do to be well prepared for Plebe Summer and the academic rigors of the Naval Academy - and not so much about what one's post graduation service may or may not be. There is way too much between now and then to have such concerns.
The bottom line: Getting prior flying experience can't hurt. It may even help a little. Is it going to be a difference maker? Probably not.