Wouldn't "Mighty Daenerys is a woman" be technically grammatically correct (although it is redundant and weird-sounding?) Perhaps it might make sense in a context when you're trying to emphasize Daenerys is actually a woman despite her might and that women can be mighty too? I don't know
In fact no, because Daenerys, as a word of High Valyrian, has a gender, just like any other noun. Daenerys is solar. The word kostōba is lunar singular, and agrees with ābra, "woman". In order for it to be understood as "Mighty Daenerys is a woman", it would have to be Daenerys kostōbys ābra issa.
The reason it isn't accusative because the verb phrase in this case is essentially one long adjective.
"Daenerys" and "mighty woman" in this case refer to the same person.
This is also technically the case in English, albeit much more hidden in modern day grammar. If someone asks for you on the phone and you're a boy, the proper reply is, "This is he" (not "This is him"). If you're a girl, the proper reply would be "This is she" (not "This is her"). Valyrian does the same thing, but with much more because the grammar demands it.