Wait a minute... Fragment damage is massively weak to both shield and armor but deals normal damage against hull? Oof.
Well, I keep hearing that only missiles have hull. Ships always have armor, even if they have no armor(since they get the 5% base armor minimum at all times) So fragmentation damage actually does 25% damage against ship hull too.
The 5% base armor is for damage mitigation calculations; it means that frag damage weapons with low hit strength will deal significantly reduced damage against hull, but high hit strength frag weapons (like the cryoblaster) will deal essentially their full listed DPS against ship hulls.
For ease of calculations, let's assume that we're firing a frag weapon with a listed 500 DPS and 200 damage per shot against a ship with 1000 base armor. 5% of 1000 is 50. Hit strength for that frag weapon is 200... divided by four because armor, so also 50. Against bare hull, it'll do half DPS (so for this example, 250). Against the last tag ends of armor, however, it'd be doing around 60 DPS - half damage from armor mitigation, and then 1/4 of that because fragmentation type against armor.
You're correct that missiles don't have armor, though.