Erm...well, I did a three week exchange program in Japan this summer, and am in Japanese 3 as a sophomore, so I guess I have some knowledge on the subject....

Here we go:

*Do Japanese student have different subject than students in Europe? What would those subjects be?
Being American, I'm not sure what classes students in Europe take! Well, there's Japanese, English, Science, Math, and besides that it varies...the high school I visited made students sort of take majors-- focus on just a few subjects. For example, culinary arts was a whole discipline. After school clubs= very different: flower arrangement, calligraphy, kado playing and tea ceremony. School sports: swimming, tennis, judo, and I think it was called "kendo"....sort of a Japanese fencing, with bamboo sticks.
*Do the students use wands, or just ones made in different style? Or would they be more likely to staffs, or some other to?
I think they would use wands. Japan is very global, and seems to take many technologies and make them their own. I tend to think wands would be more convenient than staffs, so maybe at some time wizards in Japan decided to make a switch over or something.
*I'm pretty sure that East Asian students don't use Latin spells for their magic. Do they use Chinese for their spells?
That would make sense, since Japanese kana (syllabary) is derived from Chinese characters, and Kanji (more complex characters which can stand for whole words or names) is just Chinese characters generally pronounced differently.
*Do think think there are some Japanese wizards have integrated into large cities like Tokyo, Osaka, and Kyoto? Or would they live in smaller, more remote villages? Remember, Japan is mostly urban and has one of the highest poplation dencities in the world.
I think definitely many live in Tokyo, Osaka, Kyoto, Kobe, etc. After all, there are wizards in London, and England is much less urban than Japan.
*Do you think the students consentrate on more subjects than others, subjects that might be considered more western?
I think some subjects are stressed more than others. Not entirely sure on this one, but I have to think core subjects like Math and Science would be stressed (as well as Japanese, but that's not very western )
*What could some classes be at a Japanese school that wouldn't be at a school like Hogwarts?
All the cool clubs: calligraphy, kado, origami, ikebana (flower arrangement), tea ceremony...
*How do you think they would behave socially towards the western students?
Well, when I visited Japan everyone was very friendly and open when I met them in the context of their daily lives. However, the students at the high school I visited were rather formal, and bowed many times.
*What would the teacher be like? Students in Japan are very respectful of their teachers. Do think they would have more teachers than just the headmaster.
The teacher would probably be sort of strict--not in a mean way, but not the students' best friend, either, and not so likely to say "nitwit, oddment, blubber, tweak" for a speech. I really hope I'm not generalizing here and offending anyone!
*I heard one custom where the younger students serve the older ones in the idea that they will learn. Do think they would bring some first years along for this purpose?
Yes, that's an excellent idea. My last words on the matter of Japanese school: something that made a big impression on me was the largest (and only) mural at the Japanese high school, taking up an entire wall. It was of three androgynous students, all in uniform, clutching books and looking very studious and identical and submissive. For me, that was a message about Japanese schooling (i.e., "here are the ideal students"), and said a bit about Japanese culture as well.

Hope that helps!