Lets see If I cant make this simpler and easy to understand.
Lets say your targets shield is mitigated by 50% (an easy number). You shoot it for 100 damage.
1) Without shield bypass: your shot is mitigated 50%, dealing only 50 damage.
2) At 30% bypass: Your damage is split into 70 (which gets mitigated to 35) and 30 (bypassing the mitigation), for a total of 65 damage.
50 without shield bypass vs 65 with 30% shield bypass. Those are the numbers and that is why shield bypass works.
Now earlier someone said "If the target dies without shields, the shield bypass had no effect because (x)hp + (y)shields = (z) damage." It is true that one must still do (z) damage to destroy the vessel, but that statement is untrue because shield bypass does not allow you to destroy a vessel by doing less than (z) damage, it increases the rate at which you approach (z) damage. IE it does not make LESS damage required to destroy, it INCREASES the rate of damage.
Normal Shot (100)
= 50 Damage Total= 50 Damage
100------------------------->((( Shields: 50% Mitigation
Shield Bypass Shot (70+30)
= 35 Damage
70-------------------------->((( Shields: 50% Mitigation
=30 Damage Total= 65 Damage
30----------------------------(((-------------------------------->III Hull
Anyone still not getting this?
** I should also mention that I only used the "split damage" scenario to keep things simple. In game, it does not actually split the damage, but it literally means "30% of the time your missile will bypass the shields entirely". What that really means is out of 100 shots (from assailants, bombers, SBs, Sentinels, pm platforms etc.), 30 will deal their FULL DAMAGE to the hull and armor. No other weapon can boast FULL DAMAGE because all vessels with shields have a MINIMUM 15% mitigation AT ALL TIMES. So any other weapons fired at a target will suffer a minimum 15% off their damage due to mitigation. This is the MAIN reason why Vasari are the best at killing enemy capital ships, as you focus fire on the cap, its mitigation maxes out reducing the damage being dealt to it (up to 70%, but generally 65%), but phase missiles allow strikes on cap ships as if they had no mitigation at all.
Also, one should note that 30% bypass is not the maximum percentage, Vasari subverters can increase the chance phase missiles will bypass, effectively increasing damage a lot. Its kinda like Cielos' designate target, but specific to a weapon type.