In my opinion, whether to put a pick into the vent before loading or to leave it out with the vent hole wide open to the world depends on the way the breech is designed.
On most custom flintlocks, the vent hole or vent liner goes directly thru the barrel wall into the bore. A very short, direct path.
With these, leaving the pick in the vent hole while loading the gun won't cause any problems. In fact, many think doing this creates a hollow cone in the powder charge at the vent and this hollow exposes more of the fresh powder charge to the pan flash that comes thru the vent hole so it increases the reliability and speed of the gun.
On many of the flintlocks made by the big companies like Pedersoli, Thompson Center and Traditions, the flame channel that connects the bottom of the bore with the vent hole is a rather small, long hole that the fresh powder must pass thru to get to the vent hole or liner.
With designs of this kind, the vent hole should be left open, without the vent pick in place.
Leaving it open allows the air that is trapped under the bullet or patched ball a way to escape when the ball or bullet is rammed down the barrel. In the process of escaping, the air blast will blow some of the new powder charge thru the flame channel to the vent hole so it will be exposed to the pan flash.
Plugging the vent hole with this design will keep the fresh powder from being blown thru the flame channel so, very little of the new powder charge will end up at the vent.
This same sort of thing happens with the factory made percussion guns. If the shooter leaves a spent cap on the nipple or leaves the hammer down so it is resting on the nipple, the new powder charge will often not be blown back to the base of the nipple. This can and does cause mis-fires in the cap guns.
With these "chambered breech" or "patent breech" guns, after the ball or bullet is rammed, picking the vent hole before filling the pan can create the same sort of hollowed cone in the new powder charge at the vent as leaving the vent pick in place does with the direct "thru the barrel wall" style guns.