There are two ways the plugin tries to count the pages in the files. If it sees it is a format of type "MOBI" then it uses a special MobiReader class inside Calibre. If it sees the format is anything else (currently only EPUB supported in that bucket), it opens the file using a class that will convert to EPUB.
The risk of treating a PRC file as a MOBI file is that the MobiReader does not find what it expects - because in fact it is not "MOBI" content as it knows it inside it. However opening such a file using the EPUB conversion type approach should work.
I've already got on the todo list sometime to allow additional formats to be counted which will include PRC and they will all use that latter approach. Using the MobiReader is simply an optimisation for MOBI files.