Ninjas are a doddle to get upstairs, try getting an alltec machine up there!!
I have done 3rd floor flats with my ninja in the past, done it both ways round - took the machine up and used 25ft and also left it downstairs and used 75ft. The clear winner by a country mile is lugging the machine upstairs... once you've got your breath back, you have decent suction and hot solution at full pressure which more than makes up in time what you lose in sweat. Plus having the machine at the bottom means up-down-up-down-up-down pfffff sod that!
I think it is part of the job to deal with these sorts of situations when they arise. There are ways of shaving a little bit of time off the job to account for the extra steps. Plus how dirty are 3rd floor carpets going to be? I have quoted a bit more in some cases but customers really don't want to feel penalised do they?
Depends how badly you want the work, there will be a lot of other cleaners who wouldn't charge more so you'd lose out to them if you're in the price-beating section of the market.