The biggest difference is that in an untreated or poorly treated ballast tank you have already various degrees of rusting in thickness up to about 10 mm, sometimes even more. This rust deposition contains enough oxygen to allow some of the spores to survive even though the water was deoxidized by nitrogen. Nitrogen has to be applied for a very long time to deplete—if at all—the "structural" oxygen of the rust deposits.
Secondly it may prove very expensive indeed to install a nitrogen distribution system that effectively would remove the oxygen from the water in a tank of complicated configuration. The Idea of using nitrogen is not without merits, but I am afraid it can be only part of the overall solution. The reduced corrosion by using nitrogen is subject to serious doubt; killing the bio life in the ballast water would produce a mass of dead organic material that ...