^ Why does that matter? This isn't about whether, historically, pavise shields were planted, but really about implementing that in the game.
Personally, as the post above yours says, I think that the AI should merely turn and kneel/crouch to reload, and not plant their pavise shield in the ground. Not only would it be easier to code, but the AI wouldn't **** up annoyingly.
P.S. You are correct, partially. Generally, the bolt or arrow WOULDN'T go through the shield, unless it's a pretty ****ty shield, but you also probably wouldn't want it on your back, just to be safe.
Remember, the same could be said for a shield when equipped. If an arrow could go through it, the archers could target where the arms/hands of the enemy should be, and send an arrow through the shield into their arm/hand. So, since commanders obviously wouldn't want their soldiers getting their arms and/or hands pinned to their shields, it makes sense that the shields would be thick enough that an arrow or bolt wouldn't get through it.
It is possible that pavise shields wouldn't be made as thick, due to them just being planted and not held, usually, but I still think the above ^ is worth noting.