Alright, after sleeping my head is a bit clearer.
The point I'm trying to make is that HE is also weak against shields, and it also gets worse as shield efficiency gets better. Admittedly HE does cause hard flux and as such will overload the target at some point (tactic of 1000 cuts). It is also effective against armor, but it is not able to instantly hit a target and it is not quite as easy to hit specific weapons of a target.
The biggest drawback I see with beams against high-tech ships is not their high shield efficiency (as it affects every damage the ship gets), but actually their better flux dissipation.
I'll just throw in an example (for free!) that might not fit 100%, but should get my point across: Ghost-type Pokemon are immune to Normal attacks (compare, high-tech ships are immune to Beam attacks). The solution is to simply change the attacks.
What I wanted to say with the whole "Balance" stuff, I think of it as intended imbalance. Beams are exceptionally good support and PD weapons. However, as long as shields are up, they can't really do much. Which is why I think that the Graviton Beam needs some kind of buff.
If you want to know why I'm opposed to this, just try flying the Neutrino Jackhammer. It features a Beam with exceptional range, accuracy and damage. Even though it does have long reload times, it is capable of completely destroying 2 frigates in a single burst. These frigates have no chance of survival whatsoever. None, zero, nil, NULL, 0, . It's even capable of breaking through most cruiser shields and some capital ships. Did I mention that the range is also ridiculous?
As I'm all over the place with this post, here's the TL;DR:
Beams (except for the Graviton Beam) are great support weapons. And I agree that beams are less effective against high-tech ships, however I don't see that as a problem, as pretty much everything is less effective against high-tech ships (especially with the combat skill that allows hard flux dissipation). The Graviton Beam could use a buff, apart from that beams are quite alright, with their own advantages and disadvantages, one of which is that they have trouble actually killing something.