“which means the companies that operate these ships have a hard time recovering the cost of building them.”
Actually, the reverse is true. Due to the economy of their scale they can transport cargo cheaper than the smaller ships so they get booked first. These ships are the first to have a full load.
The Cost to Ship Containers is Crashing
There's so much excess capacity in the industry right now that companies are delaying orders of new ships. Building a bunch of massive new container ships right now is like building a 500-unit apartment building in a small town with a population of 250. There simply isn't enough business to justify that much added capacity to the marketplace.