How you tallied your bonus was one of the bones of contention - which directly affects your question.
If you tally everything - skill, material, magic, etc.. then you can have a true zero bonus. But, if the item and magic bonuses are kept kind of separate, then after you have the negative mods, those bonuses can still be applied to the roll. In other words: only the actual skill bonus is affected by things like injury & vision mods, the material/magic bonuses are kept separate so they are not so affect. (Of course, the injury and other mods can put your bonus into the negatives enough so that your material/magic mods aren't enough to get your final bonus past zero....)
I go with the totaling everything up method - it is easier, and I believe, ends up being the same.