The reason is, of course, that we have yet to come up with a reliable, meaningful metric for programmer productivity, one that would apply to the lone ruby on rails coder as well as to the enterprise java cog-in-the-great-machine or the ThoughtWorks elite agile programmer in a 6-people iterative team.
Until there is a meaningful way to compare the productivity of different software methodologies, it is pointless to berate the lack of scientific studies comparing the productivity of these methodologies.
As a final nail in that coffin, I don't think anyone can claim that Google is lacking in the "let's measure everything" department, with their reputation for intensive A/B testing of every single pixel change. And yet Google has yet to resolve this problem... which would tend to indicate that this is a real, non-trivial problem, not just a case of people not trying hard enough.