I agree that segments are often more expensive than long flights. Just booked a same day turn for my husband to fly LA to Monterey and back today, yikes, that was more than he usually pays to go acros the country.
But hotels typically don't charge more per night for shorter stays. They occasionally run long term stay deals but those are pretty infrequent. I'm guessing the run of the mill business traveler whose stays average 3-4 nights doesn't pay any less per night than the one whose stays average 1-2 nights.