Moppy said:
Weapon bays might be large mounts. This would give Traveller ships a spinal, large mounts, turret mounts, missiles, and (in Mongoose) a point defense system.
I get what you're saying about armor thickness on small craft, but hit points that ensure they are disabled faster. (Mongoose gives 1 hit point for every 2 or 2.5 dtons).
Note that heavy armor is no guarantee of protection from lighter weapons. On a space craft at space battle ranges, your sensors are very important. You won't hit jackshit manually aiming at space speeds and ranges. Those sensors are going to need to be exposed to do their job, and probably don't like it when their fancy antennas get hit by lasers.
From history, Leyte Gulf saw battleships taking heavy damage from cruiser gunfire and being sunk by destroyer torpedos. I won't count HMS Hood as that was an outdated design.
"Bay" has always been an odd term for larger turrets, in some instances, and actual bays, in others. And in Traveller the 100 ton bay is the largest weapon (aside from spinal mounts). A 10k dton cruiser can have the same weapon mounts as a 100k dton battleship or a 500k dton dreadnought. The only difference is the number.
A 'small' heavy fighter at 80dtons can have armor factor 15, as can a 500k dton dreadnought. If it's just hit points then why have them equivalent in armor factor?
Actually, heavier armor IS proof against lighter weapons. Starships and tanks have heavy armor to start and are impervious to small arms. Going back to wet navies a destroyers 5' gun could not penetrate the deck armor of a battleship. It could, however penetrate the lightly armored main area of the ship, where no critical systems or areas were. So essentially the DD's only real weapon against their larger targets was their torpedoes (which Traveller does not have an equivalent, aside, perhaps, from nukes). Spinal mounts also don't have a wet navy equivalent.
Yes, sensors, airlocks and all kinds of external systems are going to be outside of your armor. However that's where you have redundancy because externally you will be taking hits. This is no different than say how a tank or armored vehicle has weak spots. But it's hitting them exactly in the right place to take advantage of that is the difficult part.
Cruisers (heavy at least) usually mounted 8' guns. The shells were insufficient to penetrate a first-line battleships main armor, but sufficient to do damage to unarmored areas. That, however, is not typical way you sink an enemy. At the same time the battleship could direct it's fire towards the cruiser and sink it with a just a few hits from it's main guns, or at a minimum cripple it. The change to all big-guns with the HMS Dreadnought meant that battleships didn't mount multiple classes of weapons any more (such as 10, 8' and 5') to engage different kinds of enemies. Whether or not that would remain true for space battles is a matter of debate, much like the switch to all big-guns.
As far as Leyte Gulf is concerned, it was a battle that was one of desperation on both sides. Even the escort carriers like the Gambier Bay and Princeton engage Japanese destroyers and even cruisers with their single 5' gun. USN DD's and DDE's also engage the enemy to protect the ships they were escorting. Their only other choice was to run, which they would do.
The Hood is an interesting issue. It had multiple faults. The first was that the idea that battlecruisers can mount battleship class weapons and be in the line of battle was a faulty assumption. Not being armored to the same level as a battleship meant they were glass cannons. The second major fault was the design of the magazine protection for the turrets. Torpedoes are the bane of all naval ships because of the need for buoyancy.

Aside from that ships that were properly built could withstand a lot of damage before they were put out of action. Even the might Bismark had a fundamental flaw in the protection of it's steering system. Many ships that were built in the 1930s, while upgraded, suffered similar flaws since naval warfare was changing and the older designs were already in place. By the time the war was in mid-stream the era of the battleship was already over.