Duncan played center much of his career. He was defending the paint; that is what a center does. Naturally a guy defending the paint is going to get way more opportunities to block shots.
That was never Malone's role. He almost never defended the paint, generally power forwards don't. That's why the Jazz had Greg Ostertagg.
It might be fair to compare Duncan's minutes as PF to Malone's and see who had more blocks. However, because Duncan played center for at least half his career, that is impossible.