I think the best argument is the 2002 Lakers v. Spurs series - David Robinson was out for part of the series so Duncan had the fun of battling more of Shaq. Shaq's stats are below:
Game 1: 9 of 22, 23 points, 17 rebounds (no Robinson)
Game 2: 7 of 16, 19 points, 7 rebounds (no Robinson)
Game 3: 10 of 20, 22 points, 15 rebounds (half game of Robinson)
Game 4: 9 of 18, 22 points, 11 rebounds (full game of Robinson)
Game 5: 7 of 18, 21 points, 11 rebounds (half game of Robinson)
Those statistics against Duncan, with no Robinson playing, are fairly compelling proof points. Now, these are different years, but they are within a band that suggests Duncan could body up in some capacity to Shaq.
For what it's worth, Duncan went 9 of 30 in Game 1 (26 and 21), and 10 of 19 in Game 2 (27 and 17). Again, narrow view and the Lakers did win 4-1, but they had Kobe.
My personal gut is that Duncan is strong enough defensively to bother Shaq out of 2 wins in a series, but the wear and tear over 7 games is too much. I'm not sure the advantage at the other positions is enough to overcome that issue.