Dear minions,
Ventilation ducts need to be too small to crawl through...
Haven't you watched enough movies to know those wretched superheroes always sneak in or escape using the vents? Just make the vents smaller so those jerks need to use the door like normal people.
If you want to avoid having your plans for world domination foiled, rethink the construction of your evil headquarters. Install smaller ventilation ducts.