I have to ask...

Mainly because it looked neat, and because fly-through hangars are so much fun ;).

(in-game, the explanation could be that this is where bigger ships dock - the Tiger's Claw in the Movie also had a top-side docking bay for that purpose, and arguably the big hole between the landing strips on the Confederation-class could also be used for docking, though there's no evidence of that)
 
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