Bypassing shield mitigaiton is extremely useful. To give you an idea, I'd say as a ship is targeted, it's mitigation climbs from 15% to 57%.
Since it climbs so fast and really the ship spends most of its time while it's being targeted at 57% shield mitigaiton, meaning any missile that can get by is a huge boost to your damage output.
Consider if you had 10 missiles that did 10 damage.
Against a target with 57% shield mitigation, you'd do 43 damage, or 4.3 damage per missile. If you had +10% phase missiles (both tier 1 techs), then that means 9 missiles do 4.3 damage, one does 10. That's a net of 9*4.3+10, or 48.7 damage. That's a 13.25% damage boost. Now, that's balanced out by the fact that some of your phase missiles penetrate shield mitigation when its rising from 15%.
Overall, yeah, they're an increase in damage. The higher the shield mitigation on a target, the more you're getting out of the phase missiles. That's why capital ships make ideal targets. Highest shield mitigation in the game. Somewhere around 70% if i'm not mistaken? Please correct me. I don't think that's right. TO be honest, I've never bothered to look, I just know it's higher.
Best thing you'll ever see is when an Advent Mothership is firing shield regeneration and you're shooting at it with phase missiles and the nanite bomb. The hull keeps lowering, shields keep rising, and kaboom. Ship dies with 1000 shield left.