I have a 14 year old boy and a no locked door policy in my house.
But I always knock before I enter, just in case. :) We have had an ongoing talk about sexuality for years now and I just assume he is, ahem, experimenting, in the privacy of his room or shower. We have talked about masturbation specifically, along with a myriad of other sex and relationship related topics.
I think you should definitely acknowledge that you walked in on him. You do not want him to be embarrassed around you. You do want him to come to you with questions - as a woman, you have opinions of the opposite sex - he needs to hear them! LOL Open the conversation with a simple - Sorry that I barged in on you - I know that made us both feel uncomfortable, but I want you to know that ....... and go from there.
Why would you say "He's going through somthing that I know nothing about"? You went through puberty also - boys and girls have the same budding sexuality and hormones and everything. So, of course, you should be able to relate with him on some level.
This is not a bad situation.
This is a perfectly normal in the life of a pre-teen (heck in the life of a male) . Don't make this a bad thing and make him ashamed of masturbating - this is all very normal and healthy. This is your son, you should push past your comfort zone and learn to talk to him about everything. What did your husband say to him? You should also be privy to that conversation - hopefully it will give you some insight and if the advice was encouraging and supportive you could always just repeat it to your son.
Good Luck and God Bless