You are also always going to need a large number of naval officers anyway, just to crew all your ships.
But if you're intentionally going for a significantly small military fielding empire then this isn't the case, and a small number of military academies would be more than sufficient for ship crew purposes in such a scenario but not sufficient enough to manage the rest of the civilian aspects of the empire.
The presentation of choice in managing such things is always better than just assuming everyone will play one set routine.
You can assign the academy an administrator or scientist as commandant, which will produce more of that type.
That's great for a more 'hack around' solution to an design limitation, but it would be nice to see some proper separation and control over the different civilian and military branches rather than just having everyone trained by the same military academies. If there are some potential restrictions in the existing codebase making it a nightmare to handle separate branches of training between military and civilian, even some kind of looser % break-up between civilian and military that the system tries to maintain within that can be adjusted in the empire details window would be a vast improvement over having dozens of leaders being generated for a branch your empire has absolutely no need in for the next 80-100 years or more.
This is kind of becoming a suggestion more than a question at this point so apologies on that, but if the direct approach of the direct separation of military and civilian academy training is a code management headache then a alternative approach could be something like the player could set a % for graduates the system attempts to adhere to when deciding if a new leader belongs in either a military or civilian branch, so if the player has set their empire training to 80% civilian focus and 20% military focus, then each new leader when generated would have a 80% chance of belonging to a random civilian branch, and a 20% chance to belong to the military branch.
There would clearly need to be some lower and upper caps to stop just setting one to some absurdly high % but heck maybe the limits of control could even be a civilian research tier if someone wanted to make it be one. So there's still no direct assignment or absolute control, it would still be possible to have a year where nothing but military leaders or nothing but civilian leaders are generated despite because that's just how RNG decided, but at least the player could properly represent things in a direct and clean manner and influence the inner workings of the empire they're meant to be in control of without using less intuitive quirky workarounds to a design issue.