No, the area behind the vents can fit a 2x2 building. So no bunkers, but missile turrets/spores/cannons can still be built. Currently space for two buildings that are 2x2. Both ends of Nydus network are 3x3.
May be worth opening that up to Nydus play though. Warp Prisms and Medivac drops can obviously take advantage of vent area, may be worth it to extend that drop lay to Zerg players as well.