Our son was accepted to several “top” universities with exactly one club, one sport, and one EC (Boy Scouts). No college seemed to have a problem with this despite the competition from his rigorous high school. Quality will always trump quantity.
Also, don’t misjudge Scouting as “one” EC when, in reality, it is years and years of many deep ECs: miles of hiking and strenuous physical activity, hundreds of hours of community service, serious outdoor and survival skills, and all the other skill sets acquired in pursuit of the many badges required for Eagle Scout. Depending on the focus and quality of your son’s troop, he should be able to show significant hours and genuine effort in many extra-curricular activities as well as leadership within his troop as he progressed toward the achievement of Eagle. For example, our son did not start a sport until high school, but his troop heavily focused on its outdoor program, and he had earned special awards for hiking (over 500 miles) and swimming (instructor level) which spoke to his athletic ability even though he couldn’t list formal participation in a single team or club sport until high school. It should be pretty easy to mine his Scouting career for ample evidence of significant ECs. Good luck to him; he seems like a fine young man.