Honestly if your horse is afraid of your tools (previously abused with them or not), you aren't spending enough time in the desensitization arena...a horse that works with a handystick, will easily be able to work with a whip and vice versa...it just may mean a bit more "homework" for you. Some horses are just more reactive too, to certain things, so that does not mean he's been abused.
In regard to the OP, I haven't watched any of his full length vids, but some of the ones I have seen seem to lend to what you are talking about...I think sometimes it's the horse trying to figure it out, and other times it may be that he does too much sensitizing and not enough desensitizing. You HAVE to balance the two, although some horses will need more in either dept. But no, I don't think a horse should be visually 'fearful' of the tools, or the method one is using. And I don't really think ANY one trainer has the answer for every horse...although I would personally send a problem horse to Clinton Anderson over most 'well known' trainers, as I have seen him in person so many times, and the horses are 180 degree turn around different by the end of the time he has with them.
I do think Parelli is good for more of the 'green' people out there, but I find his methods a bit confusing at times. I had a friend one time, try to do his 'circle' game with a horse I had at the time...now this horse would go with a point, and stop and turn with a subtle change in body position...when she did that, he was fine, but I could clearly see his confusion, when she just stood there, passing the lead behind her back, and as he was going around and when he was behind her, she would pull the line in...he was like "what?". He was used to giving his handler "two eyes", and she wasn't in a position to allow him to do that, so he kept going, and they both got flustered!
"The ideal horseman has the courage of a lion, the patience of a saint, and the hands of a woman..."