The Vulture charts that were posted use both of the same weapon only.
Another well-known setup is the Beam+Cannon. In this setup the single Beam becomes strong sustained damage for a single weapon; roughly equal over time to the sustained of the dual Beam setup due to having the same DPE (at least in theory). Note that the amount of time before the single Beam catches up to the WEP energy used by the dual Beam setup (and therefore the same amount of damage) is not at the same point the single Beam WEP capacitor empties; it is a lot earlier.
Replacing the Beam with a Pulse here isn't worth it; the amount of time until the WEP capacitor drains from the use of the single Beam (it is a fair bit more than twice that of the dual Beam) is more than enough time to take down pretty much any (at least non-player) shield - using a Pulse would just do this slower.
The advantage of using the single Beam is that you get the other slot for something else; in this case a Cannon. The idea here is that the Hull DPS (and DPE, although I have no doubt that the Cannon has very high DPE on the hull since it uses hardly any energy at all) should be a lot better than either the dual Beam or the dual Pulse - that is what the Cannon is meant to be good at, right? Indeed, the single Beam is likely to be as strong in hull DPS and DPE as the dual Beam, for any ship it matters on, due to the WEP capacitor having ran out for the dual Beam by the time it gets to the hull - so the Cannon has to be addition damage (assuming you don't miss...).
On the other hand, Pulse seems to be quite strong against hull (or at least subsystems). I am wondering if they might be too good at this, where by dual Pulse might have an equal or even greater sustained (when reloading is taken into account) DPS on the hull compared to that of a Beam+Cannon. The WEP capacitor of the dual Pulse setup will only empty a little faster than that of the single Beam; I imagine once the WEP capacitor is empty the Beam+Cannon would definitely put out more DPS than the dual Pulse. However, when there is still WEP capacitor energy left...?
Can't wait to see the hull DPS and DPE figures. Don't suppose you could do DPE for the non-energy weapons* (the ones with ammo) on the shield as well?
*[Technically, I think only the Cannon, Fragment Cannon, and Multi-Cannon are full kinetic - the rest of the weapons that use ammo are partially thermal and kinetic, especially the PA, so perhaps non-thermic is not quite the right word to use - I prefer energy weapons and non-energy weapons to differentiate between the two (officially I think the energy weapons would be referred to as Directed Energy Weapons, or DEWs), although non-ammo and ammo weapons works too].