You could say that offering all options at a discount costs them nothing. You could also argue that it does deprive them of revenues. There are arguments both ways.
It is sort of like Windows 7 home vs Windows 7 pro vs. WIndows Server. They all pretty much share the same code base (maybe less so for the Server version). The only difference is a switch or two.
If you argue that turning on the FFT and serial protocols costs them nothing, you are right! Once the scope is in your hands, it costs Agilent and Tek next to nothing to enable that feature. For Agilent, it is an unlock code. For Tek, it is a module that costs them only a buck or two to make.
On the other hand, it actually DID cost something to include those features. A lot of serial decode stuff is done hardware and software. The software costs a lot of money to develop and test. The hardware part adds some cost to every single unit sold, plus the cost to develop that test that. So, imagine that all of these extra features (FFT, serial decode, etc.) were included standard with every scope. This means that the price would have to be raised to cover all of the NRE costs. So, the price of the scope rises for everybody. For those that need the extra features, they are getting a great bargain. For everybody else, they are paying more for something that they don't need.
So, by locking features that need to be unlocked, you piss off the people who feel like the features are already there, and they are being artificially prevented from doing something that they ought to be able to do. If you unlock everything, you raise the price for the very budget-conscious customers. There is no perfect answer.