During my few years in Maputo I did most of my swimming at Club Nuval which looks out onto the ocean. It is a little small but functional. And, in the winter I was often the only person swimming in the evenings.
I would also occasionally go to the slightly longer to the Escola Secundária Josina Machel next to Jardim dos Professores which has an in door pool. It doesn’t seem like it is open to the public but it is (or was).