The center hole is not only used for determining cover saves but also is used to determine Wound allocation closest to the center of Barrage attacks which in itself implies that the source of the impact and damage radiates from the center of the blast maker, unlike standard Blast attacks which yes use the directional source of the attack.
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The fact that an Imperial Knights shields might be vulnerable to aerial or indirect fire is entirely feasible, and absent a rule that offers protections to either a top or bottom arc RAW you would ignore the shields for those attacks unless you choose to house rule it in some way.
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As I said earlier the source of Barrage damage is the center of the blast marker as far as wound allocation is concerned, and for vehicles its applied to the top or bottom in the case of burrowing attacks, which shares the same armor value as the side armor value.