I think this is back in the forums somewhere, but I had this explained to me. There are two kind of shields:

1. Normal, the ones that just absorb shit, the one that is measured.

2. Mitigation - this one's a little vague, but essentially, it's a portion of damage that's absorbed outside of the regular shields/hull. In general this is about 5%, and advent actually can up towards 10+%.

Phase missles are the answer to Advent's shields, and against TEC it only helps. Sure, a lot of the missiles are still going to hit the shields, but fully upgraded 30% of the missles are now going to hit the ship and bypass both normal and mitigation shields.

While it doesn't look like it's going to do damage, it definitely does, because you're bypassing mitigation.

Then you get even more extra damage out of them

Phase missiles that manage to phase completely ignore the effects of mitigation. Mitigation starts at 15% and goes up the more a ship is under fire, up to ~60%. Advent has a research that allows their shield mitigation to go up to 70%. That means any hit upon a ship with 60% mitigation will do only 40% of it's listed damage. Shield Mitigation stays in effect even after you take down the shields. Subverters increase the rate of successful phaseing of phase missiles. That means that fleets with subverters do much, much more damage.