Why do manganese nodules have different constitution than sea water?
Many reasons: First, the sea water does not have a uniform composition of dissolved metals. Second, if the nodule, either now or in the past, has been in proximity to an oceanic hydrothermal vent ('black smoker') then the source metal concentrations will have been dramatically different. Third, at thermodynamic equilibrium, each metal will have a different liquid-solid phase partition coefficient, and even slow precipitation isn't necessarily at thermodynamic equilibrium. Fourth, the Mn-nodule mineralogy may contain some proportion of clay with different adsorption capacities for different metals. Fifth, These nodules are lying on the sea bed, so it isn't just pure sea water that we are dealing with. There is also slowly circulating pore water from the underlying sediments. This pore water can have a huge range of composition derived from water-rock interaction, depending upon temperature-pressure history, pH/Eh, rock composition, depth of circulation and history of water-rock interaction. Finally, it is more than likely that microbial mediation is involved in metal oxide deposition at the liquid-solid interface (in which case all bets are off in respect of thermodynamic equilibrium), and almost anything can happen, depending upon microbial species, metabolism and micro-ecology.