- Admiral Ackbar
The emperor is in charge, and he wants to capture Luke and destroy the Rebellion, so he sets up a trap with the new Death Star as bait, but offering what looks like an opportunity to destroy the new Death Star before it is completed, but not making it look too easy, nor too difficult.
The second "shaft" isn't a bigger ventilation shaft, but a winding path through the unfinished structure of the base to the reactor core, which would only be possible to get to if you knew about it by heroically sacrificing (Bothan, in this case) spies to gather the plans of the base and its shield.
The emperor makes this general strategy pretty clear when he gloats to Luke about how the station is fully-operational, the shield will stay up, and his friends will die. This disappointment was evidently also part of his plan to get Luke emotional enough to turn to the Dark Side.
If they had redundant shields and/or no possible way to destroy the Death Star, the Rebels would not likely not have come to the trap at all.
However even despite all that, I think you have a good point. In particular, since flying through the station takes a long and narrow path, it seems to me they could have arranged to block it somehow. Drop a slab over the tunnel path once the Rebels fly into it. All I can imagine for that, is that maybe the Emperor realized any defense plan which could make an attack impossible, could be intuitively sensed by Luke or Yoda. Or it might be discovered by those spies that were part of the plan, revealing the whole setup as a trap.