I disagree, to do the rear window tint, they needed to take out the rear deck trim over the rear speakers, and yes, while the wiring for them is in the trunk, this doesn't preclude someone accidentally bumping your speakers, whose mounts stick up above the rear deck. You'd be talking about more like physical damage or possibly something that fell in the cone that is now rattling around or muffling the movement of the cone.
Take it back, have them check it out, if they find it was something they did, they'll take care of it, and if it was something else, be prepared to pay them fairly for their time.
My wife'* previous car was an 88 Grand Prix and the rear speaker grilles were built into the rear deck as a plastic grid. Over the years the plastic got brittle and broke, and pieces fell into the speaker cones. A shop tried to tell me my *really nice* Eclipse aftermarket speakers were blown, when all that was wrong was little pieces of plastic from the broken grille bouncing around in the cone. I disassembled everything, broke out the rest of the plastic grilles leaving just the grillecloth, emptied the broken pieces out of the speakers, and put everything back together and everything was just fine. Sometimes it just takes checking it out, taking a look, and seeing what'* up.
I think you're on the right track to have the tinitng shop look at it.
97 SE, teflon wiper blades, Dunlop Sport A-2 tires, Leather steering wheel cover, Pioneer DEH-P480MP mp3 CDRW head unit, Pioneer 12-disc changer, iPod hookup, Boston Acoustic 3 way 6x9'*, Boston acoustic separates in door pods, Alpine 4 channel amp in trunk. Magnaflow dual outlet muffler and Ractive stainless tips. Autozone rice pipe and K&N 4750 intake kit. Clear corner lights. Energy Suspension end links.