Let's say a genetically engineered organism (as large as a whale), capable of swimming and breathing underwater, have an EMP field as a form of defense against man-made watercraft like warships and submarines? Is this realistically plausible? How would it work if it did?
Many modern man-made military devices are very hardened against EMPs so even man powered EMP devices are largely impractical. Nature, especially when it comes to electronics or really anything we're "good at"is much less efficient. electric eels, for example, are only 14% efficient when converting sugar into electricity. However, with boats, and especially subs, you don't need to fry their electronics to render them useless. Subs rely heavily on sonar for navigation so if you were to have a whale to emitted "sonar" at the same frequency as the subs you could likely "blind" them forcing them to surface or risk crashing.
While something like a giant electric ray could theoretically produce enough charge to act as a NNEMP military vessels that are hardened to withstand the EMP from the close detonation of even enhanced EMP nuclear weapons aren't going to be affected by anything that small and localised. Civilian shipping might need to look out but warships are going to be in more damage from a ramming attack.