Yeah really, a 5 Km ship is, well... a bit much.
Like I think the biggest things I've ever built in the game we're a few thousand blocks and maybe, MAYBE a couple acres across. I did build a road that went on for what seemed like an eternity, but thats not exactly a structure.
I really think the biggest practical ships are going to be in the 200-500k block range as in Frost's demo of the ship engine. Once you start taking about the million block + ships, you get a little out of scale and start talking about things that will break Java at it's core. Like imagine if a 2 million block space ship crashed into a ravine? That would be ridiculous for even a very powerful computer to try and calculate, let alone the average PC out there.