I think the reasoning behind putting it in each file is a legal one. If the agreement is in each file, there is no chance of someone stumbling across a piece of code without being exposed to the license.
It may not be a good one, but all the big boys use it so if it's just visual pain, I would look for a better reason not to do the same.
If you're using GPL this is more of an issue, but if you're using public domain licenses like BSD or MIT, I don't think you really care what people do with the code anyway. I suppose it depends on how strict your license is.
