Why do PNP silicon transistors cost more to produce? NPN is cheaper?
It depends on which one is easier to produce, using the materials that are to hand. Given that most circuits can be reconfigured to accept either type, except the obvious complementary totem pole which needs both, production tends to be concentrated on the cheaper, better form.

In the bad old days of germanium, PNP was the easiest transistor to make out of the available doped forms.

With silicon, NPN is easier. 

Why is one or the other easier? It has to do with the relative carrier mobilities and conductivities of the doped semiconductor. One type will turn out to have smaller parasitic elements than the other. For the same size die, the better one will carry more current. For the same properties, the better one is smaller and so cheaper.

In an ideal world, we would like to have dopant atoms with properties that would give us excellent semiconductors. In the real world, we are stuck with the properties that boron, nitrogen and the other group 3 and group 5 elements happen to have, which just give us good ones. When we go beyond germanium and silicon, and create other substrates, the so-called 3-5 alloys, we get 'better' semiconductors, which don't necessarily have the same guidelines as for silicon and germanium.