I get sebaceous cysts all the time, just not on my willy.
If it is a sebaceous cyst then there is some minor concern for infection and abcess. If the problem isn’t treated, and the cyst erupts, it ill create an ugly, bloody crater in the skin.
If it’s a cyst, it will be a round nodule under the skin, tender and inflammed, and possibly very painful. DO NOT PUNCTURE OR SQUEEZE it. Otherwise it will ooze and weep for weeks and never quite heal.
If it gets inflammed to the point where it is extremely sensitive and painful to touch, then it may erupt on its own. You want to try and avoid this, because it can easily become infected, and it will definitely result in scarring.
I’ve found that the best thing to do is to clean the affected skin several times a day with rubbing (isopropyl) alcohol and a cotton wad. Do this as soon as you identify a new cyst. You want to dry the skin out as much as possible, to encourage the body to reabsorb the sebum.
Keep the area dry. If possible, bandage with an absorbant material. In your son’s case, make sure he has clean cotton underwear available daily, and that he uses it.
Cleanliness is essential if you are prone to these skin conditions. Prevent chafing and bathe several times a day if necessary.
Do not use any oils or lotions that can clog the pores. Avoid applying anything to the area that is not a liquid at room temperature, like creams or petrolatum-based ointments, unless you can wash it off immediately with soap and hot water.
Although Sitz Baths may not be useful for your son’s current symptoms, he may get cysts in other locations… like on the buttocks, inner thighs, or perineum. Draw a shallow bath with water as hot as he can possibly stand it, and dissolve two or three cups of epsom salts into the hot water. Soak the affected area in the hot water for 15-20 minutes.
Hot epsom salt baths also work wonders for sore, tired feet.
Do not use very hot baths if you are diabetic or have nerve damage to the affected area. You can scald yourself without knowing it.
Now, if they are clogged pores, then they will have blackheads or obvious plugs. Soak these in very hot soapy water, and encourage him to squeeze the plugs out, and any sebum trapped under the skin. Do this regularly, although the frequency may not need to be daily. Again, dedicated cleanliness will prevent these, especially after athletics, and avoid using any creams or ointments that will clog the pores.
Lord knows I would often apply creams and ointments quite vigorously to those locations when I was an adolescent… 
(But spare your son any such accusations… just casually mention to avoid those products and then go on to the next topic.)
Also, it’s possible they’re ingrown hairs, if he’s shaving the area, or the hair is breaking off. For these, you have to go in with sharp tweezers and pull the offending hairs out. It’s not fun. See a dermatologist.