Many medical professionals are misinformed about, or unaware of, BOR Syndrome. I have it, as do my two daughters, and I've had to explain our condition many times. We all have ear pits and a branchial cyst (in the neck). Me and one of my daughters are hard-of-hearing. My other daughter has passed her hearing tests so far, but has kidney problems.
Ear pits (preauricular pits) are found in people with hearing loss and with normal hearing. Ear pits can exist in people with no other abnormalities in their body. However, the percentage of the hard-of-hearing population who have ear pits (or other external ear malformation) is higher than the percentage of the normal-hearing population that have ear pits. The hearing loss is often from birth, but can also have a later onset. I would definitely get another hearing test in a few months, and have your son’s ears tested regularly throughout childhood. My daughters were both born with (closed) sacral dimples. Our neonatologist tried to find a link between that and the ear pits, but didn’t come up with anything conclusive either.
This article/study I found may be helpful (It is from 2001, but I don't really think that changes their findings): http://pediatrics.aappublications.org/content/108/2/e32.short
If you’re really worried about it, you could go ahead and get his kidneys checked out, just to be sure. Kidneys can be “checked out” via ultrasound and/or blood test (Renal Function Panel). There are also other screenings your doctor may request. Or you can talk to a doctor and just watch for signs of kidney disease, such as high blood pressure or low urine production, before getting his kidneys checked out. However, kidney disease can be a rather “silent” disease, meaning there may not be any symptoms until the disease is at its worst. Either way, I’d talk to a doctor and discuss your concerns and the research you’ve done.
I hope this helps. He very well may just have ear pits and that’s it. I just want to give you some kind of input here. At the very least, I’d keep regular hearing test appointments for your son. As far as kidneys, whatever you think is best with the information you have. I would get them tested for my kids because we know some of the family has BOR syndrome. It’s hard to say what I’d do if I were in your exact situation.
I found that the Cain Foundation’s Facebook page seems more active and updated than this website. You might find some more help there. Good luck!