In my experience, intakes are pipes at depth in order to avoid plankton blooms and surface debris and draw water at a more stable temperature. Outlets are discharged at surface.
Maintaining oxygen is only part of the requirement. The other half is removal of the products of metabolism that can become toxic at high levels. At densities required to make tank farming viable, both become something of a challenge. Any and every mechanical system used to meet the biological requirements requires a duplicate in place as backup against breakdown which can very quickly kill the crop. The capital costs add up very quickly and the operating costs, particularly for energy provide the nails for the coffin.
It is a fallacy propagated by the anti-farm movement that land based farms are viable on a production scale. There has been active research since salmon became a farm species; farms would much rather use that type of system because of the enhanced control of environmental conditions and as you suggest, the logistics. Unfortunately, the laws of biology in combination of the laws of physics mean that the laws of economics cannot be met and no amount of wishful thinking can change that. The anti-farm movement simply closes it's eyes and pretends that limitation doesn't exist.