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I don't know about the military discount, but I do know that the education & employee purchase plan discounts do not apply to the refurbished items on the special deals page. Usually, the prices on that page are less that you'd pay for the same or comparable items with the applicable discount.
I bought my MacBook Pro refurbished because it was $300 less than the EPP discounted price for almost the same computer & $500 off the non-discounted. The only difference was a 2.0 GHz vs 2.16 GHz processor - not worth $300 for me!
You can call the Apple Store to find out for sure.