Because manga serializations are censored to hell.
There's a reason why you don't see outright sex. There's a reason you don't see alcohol use. There's a reason why you ESPECIALLY don't see real-life drug use.
That whole "drunk on the vapors of alcohol" exists entirely because mangaka want to draw someone drinking but are prevented from doing so by editors. Now there are some publications, like some seinen publishers, that give more leeway for it, but in your generic shonen publication it's pretty verboten.
This is only further exacerbated by real-life Japanese youths that really shy away from underage drinking for the most part. For decades Japan had beer in vending machines with no way to authentic your age for purchase and it was purely on an honor system that you were old enough to buy it. In America, that fucker would be emptied by middle schoolers and high schoolers every single god damn night. In Japan, it wasn't a problem. That's what happens when you grow up in a very rigid, homogeneous and collectivist society. And where even people that do obey the rules but otherwise stick out get hammered down.
Yeah, the crime rate is low... but good god, I wouldn't want to grow up or live there as an American.
My man, as someone who lived in Japan, the youth use them, they just are as good at hiding it from their parents and authorities as you are at hiding that you took a taste from your parents liquor cabinet. They aren't saints, they are just like any people on earth, they are just private about their private life. Try living in a share house in Japan for a couple of years and ask them how upright they are as citizens, you will be disappointed. Hell the rigid society actually pushes most of them to be even more extreme than most of the world to try the things they won't be able to as responsible adults.
I also find your notion of shounen doesn't show drinking as ridiculous. One Piece shows drinking. This very chapter shows drinking and he acts like a freaked out child who just saw someone take drugs. Ok, if a manga is showing no drinking and use the vapors, but my issue is when they show drinking with adult characters and other characters act freaked out. At least be consistent in the same chapter. This felt more like "foreigners are such bad people compared to Japanese", why else have her drinking and him freaking out?
The honor system is more about not being a problem for others than it is about yourself. As you said, the individual doesn't matter for society, it is the same for the individual, if it is only about them, then it doesn't matter, it is why suicide rates are so high. So if they can do stuff, like using a machine so no store keeper is bothered, they will use them. And that's why the machines stop working after 11, so they can't come buy from them when the streets are empty, though I imagine some streets are still empty at 10, I know the one close to me was empty at 9.
I will agree that crime rate is low, they are nice on the outside, but they have plenty of private thoughts which are the meanest shit while wearing a smile.