I think single HP missiles are a good idea honestly. I can't imagine a projectile that's meant to explode when impacted having a tough exterior tank shots from anti-missile turrets. The way I see it, turrets being forced to have their own standalone shields, and not the parent ship forces you to just disable the turrets before employing missiles. Which is very doable. Either you'll have a few large heavily shielded turrets that can't completely take on large barrages of cluster missiles or multiple enemies, or lots of tiny turrets that can handle large quantities but are easily taken out (provided the enemy ship doesn't wreck you first).
Pretty balanced deal if you ask me. I think theoretically this will make for an interesting meta game.