Sigtrygg
Emperor Mongoose
At CERN all the particles remain inside the accelerator where they can be controlled by the magnetic fields, if the charged particles were to leave the confines of those fields they would rapidly spread,I see what you mean, but all the attacker needs to do is aim their nose up 1 degree and at those speeds they would be firing "over" the cloud at the target.
Good point about the changed ion beam in a vacuum. I think (others will know more than me) that those kinds of weapons in traveller are supposed to shoot a stream of neutrons or protons or electrons or whatever other cosmic particles, and essentially are a weaponised version of what they use at CERN (which does fire its particles in a vacuum - and has to of course).
In the vacuum of space once the particles leave the PAWS they have to be neutralised - so you accelerate charged particles but then neutralise them as they pass the end of the gun.