We should talk more about how instinctively respectful and polite the two hotheaded brothers of the bunch are. I mean, c'mon.
Before one of their first-ever human interactions, when Raph finds out that Murakami is blind, and thinks Mikey may have been a tad insensitive, he shuts that down with no hesitation. Doesn't say a word, which on its own communicates that he feels Mikey should know better because it's common sense. He thinks that this man, who he's never met before, who he knows nothing about other than he's a chef and he is blind, deserves inherent respect from his brothers.
And for his part, after Donnie and the brothers save Murakami and he offers to make them food, Donnie- through no influence of others, since he is the first to use this title, and April previously called him "Mr. Murakami" when she was telling them about the shop owner- decides to apply an honorific title "-san" to Murakami's name.
"Murakami-san, that was awesome!"
If they used the title "-san" all the time, then I wouldn't think much about it, but they don't. This is one of the few occurrences that it's used, and it's from when they're straight out of the sewers.
I really think this is a fact that goes under a lot of people's noses when they write fanfictions or the tempermental brothers interacting with others in general. If they have reason to suspect that they shouldn't like you, then they can be crass, sarcastic, and dismissive. But if you're just an everyday person? Not a threat and not on their bad side?
You can tell Splinter raised them right because they can be some of the most genuine and respectful young men on earth.
