But it's not just logic circuits - NPN transistors also predominate in discrete analogue designs using silicon transistors.

But if you go back to the days when germanium ruled (and also before digital dominated), you will see that PNP predominated; in fact, to a modern eye, schematics from that era look "upside-down" as they tend to have the negative supply at the top, and positive at the bottom!

I have before me a copy of the Mullard Reference Manual of Transistor Circuits, 1st Edition, 1960; it is full of "upside-down" schematics, PNP germanium transistors, and not a logic circuit to be seen!

What I meant by NPN being "the 'natural' polarity for Silicon transistors" was that the nature of the materials involved and the manufacuring process is such that it is easiest to make silicon transistors in NPN polarity;
Conversely, it was easier to make germanium transistors in PNP.