Pulse has no advantage over beam in energy delivered
If you have some sort of beam weapon, like a laser, maser, or proton-beam, then beam will always do more damage than pulsed, as long as the same energy is delivered per unit time of it being 'on'. Since it is the same type of weapon, there won't be any special effects to be gained by pulsing the weapon
Pulse a weapon due to limited power supply, or for cooling
An energy weapon in space will take a lot of energy. If you don't have the energy from your reactors to fire it continuously, then this is a good reason to pulse it. Charge it up using some sort of capacitors, and discharge when the capacitor is full.
Also under-appreciated is that cooling is a big problem in space. High energy reactors, engines, and weapons will generate a lot of waste heat, and you can only radiate that off into space so fast. Your big energy weapon might only be able to fire intermittently or else it will overheat. In this case, you can fire for a certain amount of time, then you will have to wait a certain amount of time to allow the heat to dissipate before firing again.
Most beam type weapons could be pulsed in the same device
There are a lot of different type of beam weapons, and even a lot of different types of lasers. Also, the kind of beam weapons that we use in space combat might not look much like the MW power stuff we have today.
That being said, lasers fundamentally work by adding energy to excite some medium, then lining up the released photons into a beam. As a general rule, it only takes microseconds from application of energy to getting beam out, so there isn't much engineering reason why you can't pulse a laser at some frequency if you are limited by power or cooling.
There are also a lot of different types of particle accelerators, which you might use to make a weapon like a proton-beam (which would be a sort of ion cannon, I suppose). Since there are so many types, I am at risk of talking about things I don't know about. However, for the types of particle accelerators that they use to generate neutrons, the beam itself is pulsed, but pulsed at such a high frequency it might as well be a beam. The pulse rate in in milliseconds. So again, there is no engineering reason you can't pulse a particle beam for a second, then turn it off to recharge capacitors or cool down before firing again.