First I will explain why you get lag with large ships on a server. Then maybe you will understand what the real issue is, and its not ship sizes.
First you have to understand how those blocks are delivered. An object when brought into an area is broken up into 'chunks' essentially regions of blocks that need to be updated and the system sends you that chunk as a data packet group (I won't cover the networking aspects). We as server admins can control the size of the block count in the chunk, and the server controls the shape of blocks sent and block types. You can see chunks in action if you make a REALLY big door with blast door blocks. When you open it you will see strips of it opening at a time, not all at once. Those are the chunks in action. I can't remember if its 128 or 256 blocks in a chunk by default.
So two ways we approach this. Smaller chunks are more efficient for network bandwidth use. The server can queue up more of them and it doesn't waste space on small updates. On the other hand more of these individual parts means that you get delivered the information a bit slower and dropped packets on the network side means those chunks need to be resent. All which slows down the processor of the server. On the other hand if you increase the chunk size the network can become more congested from the larger traffic, but it lightens the load on the server.
Since RedShift was mentioned they do have 3 Million block ships over there and they do fairly well. Koderz and SgtPepper have mostly figured out the balance of Chunks, blocks and server build that works for their community. There are tons of ways to combat the issues from the lag and most of it doesn't require reducing the data count. Data compression, reducing spike behavior, identifying laggy actions and more can be performed for the sake of bandwidth and processor performance. That is why this is best left to admins to control. Different hardware types, network builds and more come into effect here, plus population types and behaviors. For example, an RP server typically has very strict build rules, so ships are naturally reduced. PVP servers have high ship turnover which also can reduce ship size. Plus if we get more of the tools we are looking for (I want to set more diminishing returns on mechanics for example, with XML scripts to change the data on load, to naturally curb supermassives) we as admins can meet our community needs for different builds.
Plus expect to see more optimizing from the Devs. They aren't done yet and they will be able to perform some optimizations on the code to handle the amount of blocks. Plus preloading regions, better spam controls and more. This isn't a new problem with games, its been going on a long time.