Yes. On cruisers, it effectively rules out both the mid ranged shield breakers - the Proton Beam and Fusion Beam both have 24 shield penetration.
This leaves you with the choice of:
Missiles (not very effective unless you get absolutely tons of it, since the guidance disruptor is so efficient)
Plasma (do we really need more plasma spam challenges?)
The short ranged Cruiser Laser and Quantum Blaster (only really suited for rush fleets, due to the range)
It was nice when the reflective shield (was thought to have) a drawback. But now you can mix and match to get the best of all the niche shields… So this section of the weapons range is ripped out from under us.
One thing it does, is make the frigate Ion Cannon become the longest range non-plasma, non-missile, shield breaker, with it’s whopping 550 range. So perhaps we’ll see more mixed fleets, with ion frigates up front and beams at the back. But I suspect we’ll just see lots of plasma 
Of course, if high shield penetration values were made a bit more valuable by turning the mix of reflected/absorbed damage into anything other than an all-or-nothing affair, this becomes moot (and the game would get even better.)
i.e. Could be something as simple as: damage_absorbed = weapon_damage * penetration / (penetration + resistance)
Picking a suitable function is easy enough, but rebalancing the shields/weapons might turn into a big job.
Something similar for hits to armour might be better, too, instead of the crit chance. It always looks odd to me when fighters sit there for several minutes appearing to be doing nothing at all, then wham the ship goes up in a moment. The damage would build up a bit more naturally if the damage they were dealing was going up gradually as the armour depleted, rather than suddenly reaching a moment where every shot deals damage instead of 2% of them 