Knocking out the doors/vents just takes the station off-line for a little while.
Lot of political heat for what amount to an inconvience.
Destroying the air vents and entrances cuts off the inflow of air into the bunker. A good enough pasting would cut off the airflow for a few days, enough for all the personnel inside to suffocate.
Specially if we continued to bomb any recovery efforts Iran made.
That alone would set their nuclear program back years. For they would have to recruit and train a whole new crop of scientists and engineers.