when the gearbox is low on oil and the input shaft has some float in it the gearbox would be noisy when cold, this noise will also magnify when you drive the car on a long route in 5th gear - it will increase as the car covers kms over kms.
remember that the gearbox is spinning with the engine even in neutral, that is why all manufacturers recommend to start the engine with clutch pressed in.
Drain all old oil and fill with correct recommended gear oil and NOT what the shop keeper is trying to push over to you.
btw if you hear a noise only when the clutch is pressed then its the clutch release bearing aka thrust bearing as mentioned by capsat.