As long as there is anything on the planet with the Warp Gate - Reinforce, then ALL of the guard posts (including the wormhole ones) get reinforcements during each reinforcement event. As does the command station.
So when you neuter the planet, the command station and wormhole guard posts are getting reinforcements, like normal. However, the AI ship cap for the planet is based solely on non-wormhole guard posts, so they'll cap out a lot sooner. They'll still be at the wormholes and the command stations, etc, but their numbers will be capped low enough that they aren't getting barracks or launching border aggression, etc.
By contrast, if you take the time to kill all those wormhole guard posts after killing all the rest, you gain... nothing. Well, you've cleared out the wormholes from having ships sitting at them, but you haven't affected the ship cap on the planet for the AI. All the same number of ships will be there, just concentrated all at the command station rather than mixed between there and the wormholes.
Hope that helps!