There is a lot more to big-ship efficiency than just armor. In fact, probably the biggest benefit of large ships is efficient use of your most powerful officer bonuses as not only a ship captain but a subordinate commander in an auxiliary bridge, CIC, etc. has a bigger impact on a bigger ship, particularly since some of these bonuses are comparatively rare (personally I tend to see a dearth of Engineering and Tactical skilled officers for example). Bigger ships also provide the necessary rate of return to justify a "full set" of officer modules, whereas smaller ships are often better served by mounting an additional gun, engineering space, etc.
There are also numerous other component-based efficiencies. For example since a larger ship class will have fewer members, if you give each, e.g., a large active sensor then there is less replication of the same sensor capability across a fleet than if you had twice as many ships, half the size, with the same sensor. This means more tonnage dedicated to primary mission payload as well. Similar applies for components such as ECM, can apply for fire controls + ECCM depending on how you design the ship, etc. Engine efficiency is also potentially a consideration, as larger engines are more fuel-efficient and the largest engines are 400 HS (20,000 tons), if you mount multiple engines for redundancy then you can potentially make big gains in fuel efficiency and/or overall performance with ships on the order of 100,000+ tons.
That being said, bigger is not always strictly better and there are many cases where smaller ships will do the necessary work more efficiently. Smaller sensor ships or scouts are a common example. Another fairly common one is spinal lasers, as more (smaller) ships means more spinals and there is no other way to accomplish that. Ultimately, ship size is not as simple as "bigger is better" and it depends on what the mission profile and design + fleet doctrines are as well as what your race is capable of at any given point in the campaign.