It seems an additional hurdle is anti-fouling. Those barnacles and algae act as an insulator, making the cold-water cooling advantage less and less of an advantage.
(To be clear, I'm speculating without any real knowledge of this subject, and welcome the inevitable corrections.)
I want to talk with aliens as much as the next guy, but so far it seems like the vast majority of the universe is a vacuum--biologically speaking.
Which is to say: you’re thinking on the wrong timescale. Just wait and see. :)
Apart from being drawn as particles on diagrams, they violate every rule of what a particle is supposed to be.
There are formalisms where they aren't necessary, for example quantum lattice models.
On earth, matter only rushes to fill vacuums because the surrounding air or water pressure pushes it in.
My limited understanding was that 'pressure' is just a simplified way of speaking about statistical mechanics.
Maybe not. Barnacles probably conduct heat at a similar rate to water. And they create a rougher surface with greater contact area to the surrounding water. And some of them actively filter water, push it around. Perhaps having a layer of barnacles woudl increase cooling.
Barnacles and other accretive life forms means that the thermal gradient drops sharply, and hence the heat flow rate drops significantly.
Take a comparison is between (say) 25C heatsink in contact with 10C water across a boundary layer that likely on the order of 10mm thick, versus what is effectively a static fluid ~50mm thick followed by the same boundary layer.
So the unmixed fluid is going to be ~6x [1] thicker, for a heat flow rate 1/6th the original. And that's assuming that barnacles do in fact conduct as well as water, something that's unlikely (water is ~0.6, human flesh ranges from ~0.2 to ~0.5)
[1] Insert a bunch of unstated assumption about the fluid flow rate, salinity, etc etc.
I'm not sure how the MS Natick's cooling system works, but if it's anything like a ship, the heat transfer surface is NOT typically the skin of the hull (although keel coolers are essentially that, but I don't see keel coolers on the Natick hull). Instead, ship cooling systems typically suck in the virtually endless supply of cold seawater, run it through a heat exchanger (often a plate type), generally with a feshwater loop on the other side that runs to hardware to be cooled. The servers would be cooled by this fresh chillwater loop.
The above system only works if a.) you have much excess cool seawater than heat infusion (i.e. you're not trying to cool a large server farm in a stationary pond or small lake), and b.) You have means to clean the biofouling that will occur on the seawater side of the heat exchanger if left unabated. The latter, as indicated by reduced cooling capacity, may be why MS needed to stop the project 3 years shy of the objective completion date.