Is a Hercules as fast as a F-18 fighter. No.
I know the Eagle is much more agile but should it not also be much faster?
No, the Hercules is not faster, but that is due to several reasons. One, it is a prop plane, two it is a plane, meaning it is a craft built to solely fly in an earth like atmosphere (of which Earths is the most earth like you get) and it is built with a different goal in mind. The main limiting factor with planes is, in all actuality, the atmosphere, which forces certain designs if you want to achieve certain goals. A properly built jet plane will always be more powerful, more speedy and more maneauverable than a propeller driven plane, as it can go faster than the sound, which no propeller driven plane can.
However, in space there is no atmosphere and while a Type-6 is bigger and has more mass, it does not have to fight against an atmosphere, so it will just use its much more powerful engines to overcome its inertia can, most likely, end up with a higher top speed. The other thing, though, because of inertia an Eagle, being built as a light fighter and even though it has less powerful engines, can take the g-forces, which are still very much present in space, much better than a Type-6, which is built to haul goods from point A to point B. Which explains the nimbleness of the Eagle in comparison to the Type-6.
Although, one of the problems in game is the rate at which they can update positions, which is what made them limit top speed to 500 and enforce, to me, arbitrary limits on the top speeds of ships.
We could also use another analogy, rockets, a Saturn V will initally be much slower than a sidewinder and is certainly less maneauverable, but the Saturn V will have, even though it has more mass, a higher end speed.
