There are two ways it can hurt.
The first is that several people have posted here over the years that have said they are CMs and that they are not supposed to give upgrades to anyone who asks. Disney wants people to book the more expensive rooms and if information like "40% of the time I get upgraded just by asking" becomes a known "fact" on a board like this - guess what? They loose revenue because people will take their chances on asking at check in.
I have to disagree. These boards have approx 250,000 members. For contrast, the WDW resort has more than 27,000 hotel rooms on property ranging from an occupancy of 2 to 12 with the average being 4. That means on any given day there are approx 100,000 staying on property alone! The percentage of people that read these boards and take the advice to heart is a VERY small percentage of the guests that visit WDW.
Also, the resorts do not lose revenue by upgrading a guest upon check-in. Lets say they have 100 waterview reservations and 125 waterview rooms. They have 100 standard view reservations and 90 standard view rooms. Those 10 people would be bumped to waterview. Would disney lose revenue? No! They had no one paying for those empty waterview rooms. The room only has VALUE when it is booked. Otherwise an empty room is an empty room. If they have a paying guest in standard, and there is avilability in waterview, they can place them there without losing money. Look at it this way...if a hotel has 500 rooms and 400 are booked, they aren't "losing" money on the 100 rooms that aren't booked. Hotels function on the principle that they will meet an average occupancy. That can range from 100% to 50% or lower, depending on the time of year.
But the fact remains that some people have luck when they do check in if they ask....what we don't know is how many people get bumped back down quietly by the checkin CM who had been upgraded by the room assigner for asking.
CM's do not "bump" guests out of categories they have booked to upgrade other guests. A guest that books waterview is guaranteed waterview. Just because a guest that booked standard asks for an upgrade to waterview does not mean the guest that BOOKED waterview is bumped. Upgrades are given based on availability. If the category is fully booked, no upgrades to that category can be made. Also, if the CM saw an assigned upgrade they would need to get managers approval to "bump" the guest back down (I assume you are implying that the CM would do this as a reprimand of sorts, but CMs dont have that kind of power) if they asked.
The second is that several people have gotten burned by discovering what they had understood to be a "free" upgrade was put through the system as an upgrade at rack rate. I'm not sure I've ever heard of one of these being resolved in the guest's favor. So if you do ask, make sure that when you sign the paperwork at checkin that your rate hasn't changed.
I have *never* in my 22 years of visiting WDW and my 8 years on these boards heard of a situation where a guest was upgraded and then forced to pay rack rate. AND if they were billed rack rate, there is no way that Disney would charge them as they can proove that it was not the original category they booked.