Main issue with beams is that they are massively effective vs unshielded ships. This is, as you said, mainly because of the range bonus, but it makes playing anything without shields a horrid idea. Even a graviton beam can... Wear down armor unless you hit the Combat readiness threshhold.
I suppose its more that they... Are extremely polarized. In the old mod Vacuum, due to the way the hull mod system was setup, it was really common to have weapons destroy an enemy ship in a single shot unless that ship had massive durability stuff (and destroy the hull with a second shot) or else be entirely invulnerable unless you used excessively heavy weapons.
Here, beam weapons are not quite that bad, but they are exactly as bad as you claim hard flux beams would be vs shields already, Vs Armor. Armor doesn't regenerate, and hence unless you backup armor with shields, or else the armor is very high quality (meaning cruiser or heavier) then even light beams are a massive threat.
Vs shields, the polerization is when you deal more soft flux than dissipation,which causes you to suddenly go from zero damage to massive damage. That kind of thing is not really seen in other weapons. Other weapons, hard flux builds up, eventually breaking the shield. Beams, its no apperent damage until its massive damage, which I think is a problem.
Not really sure how to explain my thoughts on the situation. Still wish I could get the beam hard flux script to work...