The enemy ships will be a similar strength relative to you.
You have to watch out for the numbers advantage, still.
Phased shields will block Phased Polaron Beams in addition to regular weapons.
You currently need all of the generators on your ship to be phased in order to get the phased protection bonus.
They do work, its just that:
1) The pirates are using Tachyon Cannons (Not PPB) in stock. One of the alien races do use them, IIRC.
2) All shields must be phased in order to recieve the phased effect (ship-wide)