I see this an an opportunity, rather than a problem.
He's going to have sex, the variables are where and under what conditions.
Rather than try the futile, "trust" position, negotiate with him as an adult. He wants to have sex, presumably a lot. Girlfriend will tire of climbing in through windows.
There are things you want. I'd guess the first is that adequate precautions are taken. Maybe there's other behaviours you'd like to improve ? I'd bet money that today in a drawer is the form you got from training course that you want him to do.
He wants to bonk G/F ? Fine he turns up to the plumbing course every day.
G/F obviously has to behave well in your home.
Also g/f is a good lever for good behaviour. Relatively few girls want a drop out druggie boyfriend. The glamour of a "free spirit" wears think quite quickly.
If you are talking to her, rather than discovering her in flagrante, she might share some of your ambitions for his improvement.
Invite her over for dinner, with a nice bottle or two of wine, followed by nookie, and I think you can gain an ally.
You can be "cool parents" which she will like and may raise you up in the eyes of DS, who will know how many other parents react.
You can make his life a lot better by bowing to the inevitable with good grace. If he screws with the agreement you have a new and rather more powerful sanction.
You have him by the balls, his heart and mind will surely follow.
This can send a good message to DS2. He can learn that you can be cool parents, and that responsible attitutes to contraception etc have rewards that really grab the attention of 16 yo boys.