I must first caution that I have only seen a few eps of Strike Witches, but my understanding is the offense isn't the problem. It's the defense. There's no way a naval vessel can stand off from a Neuroi for any real length of time, given the speed of aircraft versus naval vessels, and once within plasma range a naval vessel is a sitting duck. The real value of the witches, therefore, is in dodging and shield generation.

I think you're right, though, that naval artillery can't aim high enough all the time, and accuracy at close to maximum range (which is what they'd need to keep out of plasma fire) isn't good enough to hit a target, even a large target, at aircraft speeds. Sure, one hit -would- flatten a Neuroi body (and the core if they're lucky) but it wouldn't be easy...

Well, maybe the problem is offense AND defense. XD

(edit) Also, for the like to neutralize like idea, I was pretty well convinced Neuroi craft were nanomolecular in nature. Certainly technological. I don't see any indication that they use magic at all.

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Fearless creatures, we all learn to fight the Reaper
Can't defeat Her, so instead I'll have to be Her