“Is this seat taken?”
Does it mean that this seat is already occupied?
How natives are talking for this?
It is asking whether a seat which is currently empty has been reserved by/for someone else. For example, on a train you might say to the person in an adjacent seat “Excuse me, is this seat taken?” before you sit down in an empty seat. This is to make sure that the seat does not belong to a companion of theirs who has gone to the toilet, or not yet arrived, or whatever.
Can I say: “Is this seat empty?”
This is not the normal expression in the circumstance. “empty” usually means “no one sitting in it at this moment”, which you can see with your own eyes.
The opposite question to “Is this seat taken?” is “Is this seat free?”