Hi,
isn't the upper hole the slot for passing ammo for 8,8 cm deck gun? If I remember correctly, when the "Man the deck gun" order was issued, the chain of crew members was created from the munition chamber under the officer's room, through the control room, conning tower up to the bridge. At the level of the bridge deck, in the forward part of the bridge fairing, there was a hole, which was used to pass the shells to the gunners (so there was no need to giving the ammo over the fairing).
Here is a photo:
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Regards
Maciek