If I'm in the pause menu when waiting for trades does it count towards total time

the time will never pause. time starts from first movement, and ends once the credits roll, and the real time between those two things is the time that is used

While you are on the pause screen there's no difference anyways. in java and legacy console edition (assuming the world is offline), it pauses the world as well. in bedrock, it never does, until you save and quit. Also yes, it still counts to the final time (ofc).