The reasoning behind the AP style for parenthesis is one that has to do with technology over anything else -- the brackets cannot be sent over the news wire.
From the AP Stylebook:
brackets [ ] They cannot be transmitted over news wires. Use parentheses or recast the material.Other references (notably The Chicago Manual of Style and Words into Type) make it clear that brackets should be used.
For material written in the mushroom for that paper, brackets are favorable in my mind, but when sent out over the wire can end up looking like this:
"I'm pleased to see %former President Bill#^ Clinton
has thrown himself into the task of raising money for
tsunami relief," Smith said.
After some time of editing wire copy, I have picked up what different funny symbols stand for, but they can still be a nuisance.
It might be worth checking with the person who is in charge of your wire machines to see if brackets can be sent over your wire. (That is if you care about this as an issue.)
The day will come when AP changes its style to brackets. (As soon as its wire machines catch up with the 20th century.)
Until then ...