Why would it? Once the yoyo is going through the air, it’s just a mass travelling. You can make counter-examples for the inclusion of things like vents and fins (etc) but we’re talking yoyos here. They’re not THAT different from one-another. 
Doubtful, especially when comparing modern yoyos. Maybe a really organic yoyo could drag? But you have to be at much higher speeds than even the fastest yoyoer for drag to become a factor. You’re not exactly creating vortexes with the speed of your yoyo here. It’s all a matter of scale. It stands to reason that an arrow 10g heavy will be able to move through the air more efficiently than a 10g flat piece of matter thrown with the broad side in the direction of the throw. But that kind of discussion of aerodynamics is academic when we’re comparing one yoyo to another yoyo.
You’re talking about preconception, not perception. There’s still real physics at play here. The Phenom example works because it is a fast yoyo. But if you were given a lumbering beast, even if it was angular and people told you it was fast, you might take your first throw expecting speed. But you’d find out on the first throw that it’s not actually fast. Still, I bet your preconception would also still see you throwing it faster than you would have if nobody had lied to you about its speed.
