Magazines CAN be designed from the start to work with both cartridges. I was at the range yesterday with a friend who has a CZ Shadow 2, whose magazines work with both calibers - there are different witness holes on opposite sides of the mags, marked for the caliber they represent. (He says the same mags work in the CZ 75-01, too.)

Other designs may or may not work reliably with both 9 and 40. So you just have to try each mag and see.