I'm no longer in Japan. I left in 2005. So, my posts are more or less "history," but still relevant, I believe.
As for drinking on the subway, we did it not do that often, but during my 17 years in the country, I drank on the subway more than a few times. As long as we were civil and obedient, it was not an issue.
Yes, people will just turn a blind eye to it. I don't go out of my way to do it but when I used the Seishun 18 ticket, it was just too comfortable to enjoy the view with a beer, and I think there may have been once or twice after work I was with coworkers and just stressed. Not a big deal, but not something I want to make a habit out of :-)