This method, however, will also prevent a user from installing the software if the required libraries aren't installed

Or if the required libraries are installed in some place other than /usr/include.
Maybe that doesn't happen with wiringPi, but it's happened to me wrt other modules - and there's nothing that angers me more (wrt perl) than having to rewrite a Makefile.PL because of unrealistic author expectations regarding the location of the requisite library, or of the way in which it is being made available to the compilation.
If wiringPi.h does not get found during the compilation, then the cpantester report will record an "UNKNOWN" result, and little (if anything) would have been gained by detecting the missing dependency at the Makefile.PL step anyway.

It's at the compilation phase that the library files need to be found.
The Makefile.PL doesn't need the library. IMO it should just write the Makefile according to the EU::MM directives, and if the user hasn't made the required library available to the compilation, then (s)he will soon find out.

(Mind you, I'm perhaps a bit more "touchy" about this than most.)

Cheers,
Rob