I think it's just monkey see->monkey do. As soon as one person said +1, everyone that saw it thought that that's just how you voted for stuff. It's the same reason you see comments on HN or reddit that just say "This." or that if you leave your shoes by the door, everyone else will do the same. I doubt these people keep doing it if you ask them not to.
There's an old story about this man who stood quietly next to a closed door in Moscow, said nothing to no one, and did nothing else of interest. Eventually others joined him, and before long a queue has formed. No one knew what they were standing in line for.
I remember one day I was walking through london with multiple hours to kill; and there was a massive line. Without anything else to do, I just stood in it. Approx 45 minutes later, I got to the front: turns out it was a sale for a clothing store. I didn't really need any clothing, but the discounts were good; so I purchased a jacket. This was 6 years ago and it's still my favourite jacket....
I agree that that's probably how it started, but it seems that once the cultural expectation has been set, it's hard for a single project maintainer to set a different custom just for their own project. People are going to use the conventions and communication methods that they learn elsewhere, even if you say not to in the contributing guidelines document. You might be able to get individuals to stop doing it in your project by asking them directly, but then each person has done it at least once, and you've had to ask each person to change their normal habits.
Besides, as they note in the letter, there is a valid and valuable purpose to these communications, it would just be better if they were in a different place than clogging up the comment thread.
Yeah, and now look at SO, it's got so many "rules" that you can't look cross eyed at it without breaking one of them. "You don't have enough rep!" "A minimum of 15 characters per comment." "At least 5 characters per edit." "That's been asked before." Eventually, everyone just stands in line with blinders on, forced to stare straight ahead, mouth shut, one step at a time. There's never an end once you start "tackling" these so called problems.