If it carries enough energy to burn through metal, wouldn't it vapourise all the water it encounters, and if the targetting beam is projected under the energy beam, wouldn't it stay free of the problems you mention ?
The targeting beam would go before to acquire the target and be easier to scatter - there were problems with this in some laser guiding systems. Might not even work in cloud - and this point is relevant, as I doubt they'd have developed a weapon stopped by cloud. My argument, as they say, is invalid - or at least should be!
As for the energy beam - if a target is, say 5km away, a thick mist would, I believe, scatter/absorb, deflect the beam to such an extent as to prevent it from being effective - although the analogy is far from ideal, a small cloud of an inch or so depth of vapourised aluminium over an aluminium plate plays haywire with a laser process. Same argument as above re validity. I guess......