A blower increases cylinder pressures and thus increases thrust loads on the pistons and gas loads on the bearings. On a stock-internal engine it's pushing the components beyond what the engineers originally designed them to though not necessarily beyond what the parts will take (the so-called "margin" of design.)
So yeah, lots of miles of supercharger use may result in an engine that is more worn than had it remained stock. Before buying I would, at the very least, make the deal contingent on a successful compression test and if that's okay, do a leak-down test when you get the car home.
Thing is, 4.6L 2Vs are common as dirt and cheap. Even if the engine is tired but you like the rest of the car, consider that you can replace the long block for very little.