unfortunately yes .  Sometime back they changed all ship blueprints to use "best defense" which is whatever type you have researched the furthest of has the highest value. So if you get tier 1 shields, your ships will have shelds, then research PD to tier 2 and all designs change over to PD, research up to tier 3 armor and everything new comes out with only armor.  The exception is each hull at med and up has a "balanced" design that uses all 3 weap & def in their build.  I modified the default blueprints to give me 2 "best" for every 1 of the other types (that i have researched) .  Otherwise design your own on the fly as needed based on the weapon load out of the AI you are going to fight