High damage (hurray for accuracy enhancers!) over high rate of fire for the same damage per second is significant only for one-shot player kills. For example, two weapons which inflict 3000 max dps:
PvP Smackdown Hammer has a 6 second recycle time, and max 300 non-crit damage/hit.
Hunter's Little Tool has a 1 second recycle time, and max 50 non-crit damage/hit.
For PvP, overburn expenses and the wait time to use a healing tool are of much less concern than overpowering the target's defenses (armor) and killing the target in one shot so that the target has no opportunity to use an uber healing tool. Hunter's Little Tool, for example, would inflict at most 1 point of damage upon anyone in decent PvP armor, like Eon (L).
For hunting defenseless creatures, high rate of fire wins every time because you have a shorter wait time to use a healing tool. Also, you can limit the amount of overburn for ammo and decay. (By defenseless, I mean creatures which bear the full brunt of all damage dealt upon them.)