They want to return the first stage to land in the future (at least when possible, depends on the launch trajectory etc iirc). So high waves won't be an issue when they start returning the rocket to the launch site.
Also, I guess if reuse becomes routine and they need to land in the sea (because there aren't enough fuel to return to land) they could build a huge vessel capable of handling high waves.
Also, I guess if reuse becomes routine and they need to land in the sea (because there aren't enough fuel to return to land) they could build a huge vessel capable of handling high waves.