They're using the ships to create a patchwork of anti-air defence in the hope they can stop things but the size of the area to cover is simply massive and it's very easy to fly missiles/drones around the perimeter of the ships with a little intel.

Iran has satellites and their own launch system for satellites so my assumption is that they have fairly good intel on ship locations in the area, provided to the Houthis by Iran. This is the only logical way they could be as successful as they have been.