In the 2.x quests (after Operation Super Duper Original Endgame Content), they're treated as still being held. The hit that was done in OSDOEC seems to have only destabilized the Castrums, or killed everyone originally in them, prompting the Garleans to send more. To unlock the Binding Coils, you have to kill your way into Limsa's Castrum in order to survey the dig site, and during the Crystal Braves storyline, you have to stop someone from fleeing back to their Garlean masters within the big Castrum in Northern Thanalan, and have to save one of your fellow Braves from being captured in the Castrum in Mor Dhona.
When the Doman children ask what Mor Dhona is like during a cutscene, you have the option to tell them (in a rather reluctant way) that Revenant's Toll is a "stones throw away from an Imperial Castrum," implying that it is still a danger, and very much active. You also bomb the crap out of some of their supplies to sabotage their efforts a few quests later.
It's therefore safe to say or assume that most of the Castrums have been remanned and restocked.
When the Doman children ask what Mor Dhona is like during a cutscene, you have the option to tell them (in a rather reluctant way) that Revenant's Toll is a "stones throw away from an Imperial Castrum," implying that it is still a danger, and very much active. You also bomb the crap out of some of their supplies to sabotage their efforts a few quests later.
It's therefore safe to say or assume that most of the Castrums have been remanned and restocked.
