I don't see any problem with those uptakes, here we are talking about jet-engine, and they can literally b placed anywhere.
I have seen ships whit them placed in the bow, ships that have them placed on the upper-deck/roof. Hell I even have seen a ship that had engine problem, received an generator container, that was placed on a cargo deck, then all the power from that generator was sendt down to electric motors. It's not like the good old days with heavy diesel engines or steam power plant, that was bound to one place in the ship.
If the engines, as you say can be placed anywhere, than consider, the length of the shafts of propellers from the engines, or the uptakes tubes inside the ships, not to mention the intakes tubing, these use a lot of space.
You also need a clear space above the engines to take them out and replace them, as you don't repair gas turbines (jet engines) in the ship. They are being replaced, thanks to their comparatively small size.
you are so yesterday. we do this quit often in Norway, and shaft length is no problem at all. we have car ferries with shafts that are 80 meters long! what they do is having the shaft trough several joints, that mean that even if the ship bends...
you don't need shaft, only from the electric motors. all you do is connecting the jet engine to an electric generator (small fishing boats her in Norway use hydraulics) then run a couple of massive cable trough the ship to the electric motor. for example ramform ships. they have there engine mounted in the bow, over waterline. do they have an shaft from bow to stern, no, there engine is powering electric motors that again is powering the propellers.
the you will say that electric generators can't take the rpm from an jet engine, well gears. look at the Nansen class, it is CODAG, but not the Normal CODAG you are used to. it have several gears making the ship to be able to have it engine to drive the shaft directly or trough electric motors, and all engine can drive separately.
so no long shaft is needed, but a long shaft is not a problem at all. Ebba Mearsk for example have a 120 meter long shaft, you loos some on friction due to length of shaft, but you save that in, because you will be able to design a more balanced ship with better hull.