I think it depends on the person, and probably the age as well. When my friends and I went to the MAM store in Harajuku, we thought the shopkeepers were absolutely adorable, and we hugged them when we were leaving. They didn't seem to mind (of course, we also bought their stuff), but I doubt you'd get much more than a weird look if you went up to someone on the street and asked for a hug, haha.
If you know them, it's probably not a big deal. Especially in terms of 'goodbye's and whatnot--it's a very emotional time. So you should be okay.
