It does have an effect. What's never been clear is exactly how it works.
For example, what does a "99" mean for pitcher fatigue? Does his walk rate go up 1%? His OAV 1%? His HR/9? All of them? Some combination?
Similar for hitters: does BA go down by 1%, walk rates, OBP, SLG, or what? What about as fielders?
There are some owners who want a pitcher showing any fatigue at all to suddenly become worthless. Maybe they're right, I don't know.
But consider Milacki for a second - lowest OAV in history for any pitcher with 25+ innings - he gave up 9 hits and 9 walks in 91 plate appearances. OAV of .110. Suppose 90 fatigue means 10% worse OAV...so that's .121. 20% worse would be .132. 40% worse (60 fatigue) would be roughly .154. A pitcher with an OAV of .154 is incredible...there are only 47 pitcher seasons in the entire WIS database with an OAV of .154 or better.
Even if his walk rate, HR rate, and other stats that go into the "outcome algorithm" used by WIS also decayed by 40%, he'd still be pretty incredible.
Now again, I'm not sure this is how fatigue works, but it's certainly possible. And note that for a pitcher with an OAV of .200 (still really good), pitching at 60 fatigue would mean an OAV of .280....which would definitely be noticeable in the SIM. For a pitcher with an OAV of .300, 60 fatigue would mean an OAV of .420, and he's going to get lit up by a Christmas tree.
So it's just possible that WIS's fatigue model works fine - but in extreme cases like Milacki it breaks down.
I would definitely not want to see a model where all pitchers suddenly become equally bad as they fatigue. A fatigued Pedro should still pitch much better than a fatigued John Burkett.