Fair enough. The rest of your post was talking about Pathfinder, so I thought you meant the Pathfinder Ninja (and TBH, I had forgotten the 3.5 Ninja existed).
"A deflection bonus equal to your Charisma bonus" and "your Charisma bonus" are not the same thing. You could have 1000 of the former, but you would only get the benefit of one due to the stacking rules. You can only ever have one of the latter, so there is no need to invoke the stacking rules.