Well, haven't you noticed how slow this forum is getting? Do you know of any 3.5 sites that still go strong?
Regarding ability penalties and ability damage: I think it's rather straightforward. If you have Str 13, take 6 points of Str penalty from being exhausted, and take 9 points of Str damage from a Shadow's touch, you're now at Str 4, effective Str 1. The Str damage directly reduces your ability score, while the penalty only modifies your effective ability score.
A more interesting question would be: If you get a Str bonus from somewhere, does it still apply when your base ability score is reduced to zero? For example, you're Str 13, under the effect of a Bull's Strength spell, and get Str damaged by a Shadow for exactly 13 points. Do you die and turn into a Shadow immediately? Or do you die and turn into a Shadow once the spell's duration runs out? What if your Str damage is greater than 13 points, but below 17?
BTW: similar questions could be asked concerning temporary HP, although these don't represent a "bonus" in the technical sense of the word.