Maybe they just didn't want her around - I listened to the commentary track on Dogma, and while Kevin Smith complemented her work, he must have mentioned at least 3 or 4 times that she was terrible to work with.
I was surprised that she isn't around this time as well. When the subject of a sequel was first seriously discussed last year she joked that she'd probably be the only one of the original trio to return - because Will Smith's and Tommy Lee Jones's asking price had gone up so much on the strength of MiB and other films.
It may be that there wasn't enough money left in the budget after hiring the other two to include the lovely Linda as well. Or maybe it was a scheduling problem. It must have been tough enough to find a slot when Will Smith, Tommy Lee Jones and Barry Sonnenfeld were all available, adding Fiorentino to the mix may have been too much. (Remember how much of a problem scheduling has been for Indy 4 given all the other commitments of Connery, Speilberg and Ford.)
I wonder if they'll explain what happened to her character. Maybe she went on a different mission or something while Will Smith's character is assigned to bring back Tommy Lee Jones' character. Doesn't look like her character will be that important to the plot anyways, so maybe that's why they didn't re-cast her.