Q: Do my feelings about whether my horse is smart or not, or good or bad, and if that should affect how I train or work with him?
A: I believe horses can certainly perform up to, or down to, our expectations.
If we look at this from a research perspective, we know very well that experimenters' expectations of their subjects and their desires for certain outcomes can affect results. This is why some of the very best research is done under "blinded" conditions. This means the experimenter doing the work doesn't know what treatment the subject has been given, so that he can't measure or score findings either consciously or subconsciously to get the results he is hoping for.
More to your point, there's been some work to show that experimenters can be biased about their subjects and affect the outcome of their research. Awhile back, psychology professor and researcher Dr. Rosenthal of the University of California, Riverside, showed that if experimenters were told they had either smart or dumb rats (and there was actually no difference in any of the rats' intelligence!), those rats learned a maze test better if they were supposed to be "smart" and poorer if they were supposed to be "dumb." So the rats seemingly performed up or down to their experimenters' expectations.