For kicks, I just went through all of Keep on the Shadowfell and Prince of Undeath (the lowest and highest level published 4E modules, respectively) and added up all of the creatures/traps that attacked each defense.
Interesting results.
In Keep on the Shadowfell (the revised version), I found that MOST creatures just attacked AC. As for the other defenses, these were the tallies:
Fortitude: 10
Reflex: 23
Will: 2
Interestingly, every one of those creatures that attacked Fortitude, except for ONE, also attack Reflex. Also, the two things that attacked Will were both in the very last encounter, so there wasn't a single Will attack through the whole adventure prior to the end boss fight.
But most things only attacked AC, and I felt like the adventure had a very representative variety of low-level 4E monsters.
Prince of Undeath was VERY different.
In this one, nearly every single creature attacked at LEAST one of the NADs, and many of them attacked more than one of them. Here were the tallies:
Fortitude: 81 (50 non-minion)
Reflex: 96 (59 non-minion)
Will: 33
Those numbers for Fortitude and Reflex include the 31 and 37 minions, respectively, who attacked those defenses. So if you don't count minions, it's 50 against Fortitude and 59 against Reflex.
So, judging just from these "archetypal" modules at the lowest and highest levels of play, it's clear that Reflex is by far the most common at low levels, and slightly more common at high levels. Will is almost non-existent at low levels, and still significantly outnumbered at high levels. I was surprised by this latter fact, expecting to see a lot more Will attacks at the upper level.
These numbers are not "weighted" at all based on attacks from elites or solos, so that might skew the results if such an analysis was performed. (For example, the Empowered Orcus at the end of E3 only counts as 1 under Fortitude, but some more mathematical breakdown of the "significance" of each attacker would probably count him as more.)
So, there you go.