No, Disney does not generally discount rooms at check-in. Their discounting process is to identify resorts/room categories that aren't booking some months in advance, and then offer a limited-time discount offer on some limited number of rooms. When that number of discounted rooms is booked the discount is gone, and it's back to rack rate. So, your best chance at snagging a discount is to watch for discounts well in advance of your trip. Our Discount Codes & Rates board can help with that.
As for free upgrades....Disney doesn't hand those out for the asking, either. Front-desk CMs don't have the power to hand out free upgrades at will. As a rule, complimentary upgrades are assigned in advance of your arrival, and they're done for the resort's operational needs. They're also not nearly as common as one would think from reading these boards.
From what we've been told by CMs posting here, on the occasion when they do have an upgrade to give out, they'd much rather surprise a guest with it than give it to someone who walks up and asks for free stuff.