Do school-wide holidays count against personal vacation time?
This is not meant to be an official opinion, since obviously the rules depend on the local labor laws.


We should distinguish school holidays—days on which classes are cancelled—from official holidays, on which the university offices are closed.
A graduate student not working on a school holiday would be counted as taking leave; however, when the university is closed, that is not normally expected to be a working day for anyone, and thus students would not use a vacation day in such a case.
Advisors should not have policies in place that expect students to be regularly working six days a week, particularly since that would mean that they are potentially in violation of a whole bunch of labor rules.


Given that information, my personal opinion is that research cannot be done according to a timecard. There will be days when you go into the office and figuratively spin your wheels all day, and there are days where you are firing on all cylinders and getting tons done. In my own group, so long as someone:


is prompt in answering requests, 
attends group functions, 
lets me know if he or she will be out of the office for extended periods, and 
is getting his or her work done,


then I will let that person work in whatever manner is most conducive to getting the job done. That's more important to me than knowing they clocked in 8 hours per workday.