Capital ships are like the Yamato in WW2 in a way.
Too valuable to be sent into risky situations but too powerful for enemies to avoid.
Pirates can't really attack Manhattan for a few reasons, including the large capital ship patrol presence. They don't usually have the firepower to deal with such large ships.
Hence their usefulness in defence.
Anyway.
I would suggest using large freighters.
Clog up space, a lot of it.
