Doesn't matter what engine size or the number of cylinders you have...You could be running a 1000cc street-bike engine in your quad and still get beaten by something else. Top speed is determined by the final drive gear ratio on the machine, and of course by how high your engine can rev and still make usable power with said gear ratio. Assuming that two quads go to race and are geared the same, the quad which can rev higher and still put out HP will win. In theory, at least. (This doesn't take into account drag coefficient, rider skill, and other real-world factors).
Example: A 1000cc street bike engine'd quad would outrun a Banshee on the top end, even if both quads were geared the same, because many of your little inline 4' bangers keep making power even past 12K RPM's. Unless you've got a Banshee with some wild motor work and porting, you're pretty much done with power output on a 'shee by the time it hits 10-11K. As far as I know, that is. The 1000cc quad wins this drag race, at least on paper.
I'd say in real life, it all boils down to the gear ratos used on the two quads racing each other, type of racing (drag vs cross country vs MX, etc), the respective power outputs of the two engines, and who is the better rider when racing a 'Zilla vs a 'Shee. Both quads are beasts; I've never owned a Zilla so I can't fairly compare the two. Pretty sure a Zilla has a Banshee beat on HP, even after adding all the common bolt-ons to the 'shee.