The most important thing to get into any science related graduate program is research. A cherry on top is research resulting in publications. If he wants to go to graduate school, he was smart in “sacrificing” internships for research experience. In science, research experience and especially publications are top currency. Clubs/leadership positions really do not matter.
With respect to soft skills, at my grad school we are required to take a writing class and a class on how to give a presentation/seminar/chalk talk/elevator speech. We have seminars on networking, finding an internship (if desired), grant writing, identifying careers of interest and how to tailor our graduate experience to obtain those jobs, work-life balance, etc. My school exposes us to all kinds of science related careers outside of just being a PI and staying in academia. Granted I am in the life sciences, not physics, but I would think it would likely be similar.
I also think that the point at which one is looking into grad schools is a good time for parents to let their children take the reigns. Grad school, especially in the sciences, is extremely different from undergrad. Plus, each field is so specific that often only someone in that area of interest can really select which schools are best for him/her. The person who can likely help your son the most is his undergrad research PI. He/she knows the field and may be able to mentor your son throughout the application process.
Graduate schools will welcome students with very high grades, GRE scores and accomplishments such as research/publications. You seem worried that your son may not be making the most of his conference contacts, but his academic record is what will get him into a graduate programs. “Contacts” can help, but academics come first.
Obviously, what employers are looking for depends on the employer and the nature of the job. Some will demand a high level of independent work, others will need someone who can work well in a team. But just because your son may seem “lonely” doesn’t mean he can’t thrive in a collaborative work atmosphere.