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It is an imperfect implementation of the reality that sometimes you don't need all your buildings active. If you aren't building Magisters you can save 10 gold/turn by disabling the Military Academy.

You will notice that you can't upgrade units if your higher structures are disabled (ie, can't upgrade Mages to Magisters if the Military Academy is disabled), but you can still build Magisters outright. Hopefully it is fixed/made consistent in an upcoming patch.

Right now, there is nothing stopping you from micromanaging your buildings on/off and still reaping there benefits.
 
There is a lot of actual benefit to disabling buildings in the late game. A lot of the research structures are useless once you have all the spells researched, such as the Demonologist's Workshop and Excavations.

As far as still being able to build the units, well, I agree that it is goofy.
 
It is probably the bug, since all other features are disabled, when building is example. For example, disabling resource buildings disabled ability to add perk. Or when Military Academy is disabled, you can not do upgrades to higher levels units.