Windows is an OS that allows applications to communicate with hardware. Nowhere in this layer is there security to ensure that the applications are genuine. The applications themselves must check themselves for genuine status. The only thing that may happens is the application calls on the OS to check for updates on its servers, but ultimately this responsibility is on the application. Windows provides no guarantee that it will detect any unauthorized software other than the OS itself. This is true for all OS.
Windows uses WGA which checks windows itself, not other applications.
Plain and simple, Windows has no right, responsibility or motivation to check for unauthorized copies of anything except Microsoft products. Even then, quality pirated software will bypass any filters set in place, for example pirated versions of MS Office update fine on Windows as the pirated Office is well done. On the other hand, Adobe products must block access to their update servers so that the OS cannot direct updates to the applications that will flag them as unauthorized.
While you have no control over your customers, you can assure them that the windows you are selling them is valid and will not interfere with any illegal activities they decide to be engaged in unless it invalidates the copy of Windows that you've sold them.
It is difficult to prove a negative so it's going to be near impossible to find documentation that MS Windows will not check for pirated versions of other software, especially if the software manufacturers decide to partner with Microsoft in the future. Currently, though, this is not occurring.
Remember to remind them to support software developers if they like the product they're using. Additionally, there may or may not be well-enforced penalties associated with the usage of pirated products depending on the location of your market*.