Ultimately, the puzzle solving aspect of the Zelda games is more important than presenting a version of time travel which "makes sense". Since it's generally assumed that players will understand that, and therefore not think too much about it, I can't imagine it's ever been explicitly addressed.
That said, it's not time travel in the traditional sense. It's essentially a localised shift of the time period within a specific (generally small) area, but there's nothing to suggest that it has to - or does - apply to everything.
It's possible that whatever magic the timeshift stones use doesn't apply to things that have been interacted with in Link's current time, so using a key to remove a lock on a door in the "present" means that the lock doesn't get restored when the timeshift stone shifts the time period of that area.