But in answer to "how would this work"... I'd say if someone is going to crawl ON the ductwork, you'd want to put the PIR above said ductwork. Realistically, there's usually going to be fairly limited areas with enough room for one to move about in a ceiling, whether it's above or below tin, between tin, between pipes.
There will probably be only one or two choke points between areas where they could enter (outside-accessible washroom, roof hatch, etc.), and areas of the store they'd want to access (storage room, office, etc.). Identify those choke points, and cover them.
Alternately, you could possibly add a couple cheap cameras up there, and set them to trigger either an internal I/O, or an I/O channel on the DVR, with just basic motion detection set to low sensitivity. You'll normally see little to no significant motion in the ceiling space, and any major change of lighting, whether from someone with a flashlight or someone opening a tile, will register as "motion" to the camera. Unlike a PIR, that needs an unobstructed "view" to work, a camera will register the change in scene anywhere within its FOV.