The header/footer scripts is a hard one to grasp, only when related to social sharing (i.e., user inputting facebook app id for rich sharing/fb likes) implementation with posts as a specific use case I suppose an extensible theme with actions that a plugin could hook into, to place the social sharing icons/buttons is what is recommended, but this solely depends on the plugin itself being extensible as well. Extensible as in, I want to control 100% of how the icons/buttons look and operate.

In a sense, relying on a 3rd party to provide social sharing in your theme, and make it look good, is risky.

Knowing this, it's easy to understand why this particular use case is common in themes. Why muck around with finding the perfect social plugin to compliment your publicly distributed theme, and take the chance of the plugin either messing up, or straight making the theme look like ass, when you could just as easily build it in yourself.

It'll be interesting to see where this goes. While I do agree that functionality is best served in plugins, there is still some justification for theme based functionality, to a certain extent.