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I'm only halfway through my first campaign, but the 2 effects I've observed are:
1) At certain levels, new national ideas for military organization become available.
2) As the tech increases, you get a random chance and a number of events, which might do things like a permanant increase in all army's discipline, etc.
Land Organization (and Naval Organization, too) determines the rate at which morale returns to units that have less than 100% morale.
That means the Military Camps national idea should significantly improve how quickly the morale of your armies improves after battles. I haven't tried it with the most recent patch, so I'm not sure how it impacts the "armies with low/zero morale get annihilated at 2:1 odds" game mechanic.