Actually, a number of people do ask about upgrades at check-in. Some of the reasons have been covered here and they include the fact that it is standard operating procedure at many other hotels (and even at Disney's own cruise line), discounts have been offered in the past by Disney and given to those who did ask at check-in (specifically the few years following 9/11 and surprisingly at the WL, where for about $25 a night, you could upgrade to their club level at check-in) and finally, some guests find themselves with a little more money to spend when the trip actually arrives.
When you consider those things, the question being asked at check-in is not all that out of the ordinary. Whether you're asking what the rate is within the initial question or as a followup, doesn't really matter all that much to me ;).