The main reason is that a 100% viewfinder requires extremely careful adjustment to assure that the framing in the viewfinder exactly matches what will show up on the sensor. In most cases (I'm pretty sure all cases, really) this means they have a little adjustable frame just below the pentaprism that gets adjusted by hand to match up precisely with what the sensor sees. That kind of finicky hand work costs serious money.

The other part is that a 100% viewfinder requires that you build most of the components in the viewfinder optical path a little larger to allow the larger stream of light through. With a 96% (for example) viewfinder, you can make the view-screen, pentaprism, etc., all just a tad smaller saving a bit on materials and such. This undoubtedly makes the biggest difference to the pentaprism, since increasing the area of the viewscreen requires increasing the volume of the prism.

In theory, it's not really related to a pentamirror versus pentaprism -- if you wanted to badly enough, you could (theoretically) build a pentamirror camera with a 100% viewfinder -- but it would be a little like a Tata Nano with a diamond-crusted shift knob.