I don't think Manaka will wake up simply because they took her from the sea god and brought her to the surface. That would be too easy. I suppose it does provide a different reason for the ED if she does. It's not that she woke up decades after the others, it's that she can't live underwater anymore.

I also think it was Manaka herself that was guiding Miuna around. Not just because she accidentally said her name when guided by the ena flakes, but because Manaka was her friend too and wanted to be reunited with the lot of them.

The only reason I can think of for her ena eroding is that she's a sacrifice to the sea god. She has to drown, like the original bride/sacrifice for it to count.