Stock boosters aren't that bad balancewise, even with a full stack of them. Engineering taking them from a 20% boost to a 70% boost is what makes them crazy.I'd support a shield nerf. Boosters loose 50% of their strength across the board.
Capping resistance resistance buffs at the largest individual booster in each category, and the total shield multiplier at "the largest individual booster or the total unmodified boost, whichever is greater" (ie. allow unengineered boosters to stack) would limit them pretty effectively and people wouldn't feel as bad using a couple of utilities on point defence to deal with those pesky missiles.