Flying over north pole became quite popular due to great circle routes going that way. use of GPS in civilian aviation actually came from compass getting confused during polar flight resulting in heading reversal. GPS satellites also supported polar operations from the start as the critical user needed flights over north pole. (this is one of those cases where typical map projections confuse people).
That said, magnetic compass deviations are common all over the world due to things like iron ore veins, so maps have corrections available.
GPS isn't used for altitude in aircraft in practice, it's too inprecise - barometric altimeter plus radar altimeter are the precise instruments for that.
