I don't think high penetration lasers are a benefit to game play.
A laser would have low penetration, and in this case gameplay agrees - high penetration lasers are bad for gameplay as they make lasers the only really viable weapon. Laser down their shields, target power plan, kill target. You might have a back-up multi cannon or cannon, or a heavy hitter like rail guns or plasma accelerators, but everyone uses lasers as their main weapon because they kill shields and have high penetration.
You are absolutely right. The most effective loadout this days, is gimballed pulse lasers. The cheapest weapon, is actually the best: most effective, uses no ammo, generates low heat, has good shield damage, and great penetration... This is nonsense from a gameplay point of view. Balance comes from limiting some aspects of the weapon so it does not perform well in every aspect.
Take, for instance, railguns:
+ Good damage to shields and hull, extreme penetration.
- Expensive, no gimball, low ammo count, very hard firing mechanic
Or guns:
+ Good hull damage, average price, average ammo count, gimballed
- Slow projectile speed, bad shield damage, limited ammo.
Beam lasers are somewhat balanced:
+ Great shield damage, good hull damage, average penetration, gimballed
- Very expensive, extreme power requirements, high heat generation
Then we have Pulse Lasers:
+ Cheapest weapon in game, good shield damage, good penetration, average hull damage, no ammo, low heat generation, gimballed
- ???
We could do with some weapon rebalance, namely pulse lasers and missiles (also named uselessiles)