A husband works at sea or as a long-distance driver and rarely comes home. How is the rota counted?

Time spent at work is not counted in the rota; when he returns, days ashore are divided fairly between the wives, and if one wife accompanies him to work, use lots or agreement.
Allah does not burden a soul beyond its capacity (al-Baqarah 2:286), yet fairness remains obligatory in the time available (an-Nisa' 4:129). The Prophet ﷺ drew lots for the wife who travelled with him (Sahih al-Bukhari 2593). Suggestions: record return dates and divide days ashore equally; if leave is short, continue the rota from where it stopped last time, rather than always starting with the same wife; use video calls fairly with all households while away; and make sure each household's maintenance is sent on time. Also consider whether such work makes fairness possible before taking another wife. See the question on making up turns.