Chris, thanks for dropping by. I think there are three main reasons for avoiding non-commercial licenses.

1) People not re-using because you have inadvertently limited their use. As you note there is the opportunity for individual relicensing.
2) People using automated systems for large scale aggregation not using your material. In this case the costs of manually clearing special licenses aren't worth the effort. As we move to an "intelligent" web this will start to become a serious problem. This is the technical problem that most worries me, that our ability to do this will be still born because of license issues.
3) You limit the flow of money back into the commons by effectively dividing it into two parts, one where people can make money and one where people can't. The one where people can't will just wither away in all likelihood.

You say it yourself. "Lost use....Unknown". This is a classic tragedy of the anti-commons. It is probably feasible to put some reasonable bounds of the amount of money you lose as a result of enabling commercial re-use and in most cases this is pretty small amounts. We have no idea of the opportunity costs caused by restrictive licenses but the evidence appears to suggest that across the system the losses outweigh the potential gains (not necessarily to individual players though).

In the end, by not putting materials into the commons you reduce the rate at which we are creating this new economy and enabling business models that work in it. This economy can only work if transaction costs for rights negotiation are near zero and by using CC-BY-NC you actually raise transaction costs for commercial users. Not a problem on single transactions but if you're talking about single transactions then how much money are you really going to make on them anyway? The money is in volume.

The Open Knowledge Definition explicitly excludes non-commercial terms because they have this effect of "splitting" the commons. Explaining why this is bad to corporations and individuals trying to make money is going to be hard and take a while. But I would argue that for publicly funded institutions where the mandate is to maximise total economic impact, and not income (or at least I would hope that's the mandate anyway) the argument for me is pretty clear.

Blog post incubating on this - I don't think I've got my arguments fully sorted but I think this is probably the most important debate of the next 12 months in some ways.