Hi there,
In Japan Christmas is celebrated somewhat differently from how it is done in the west, for instance the First day of Christmas is not a national holiday but the day before is, because of the Emperors birthday. Also schools are free as of the 22nd so you will see more people travelling that during normal times.
Still I think you should have no problem finding seats to sit together with your party of four, if you reserve on time. The great thing about the JRPass is that you can start making reservations for your whole trip, the moment that you exchange it. So when you do this, I would suggest that you make your seat reservations then too.
Also if you plan to dine out on Christmas Eve make sure that you reserve a table in advance as this is the day that Couples take their loved one out for a romantic evening.
Hope you have a great trip in Japan and don't forget the check some of the light displays, they are very beautiful!
-Daniel