Just tested the E5S dummy on my NIN in unmelded Eden Normal i480 body gear, Neo-Ishgardian Daggers with three DH melds, and Neo-Ishgardian i480 jewelry with two melds per piece. Killed it with 18 seconds left. All I did was use Bunshin manually, and she killed it fine without Hyoshi Ranryu (she just did 30% buffed Raitons) and no Meisui’s. *shrug*
So in my opinion, NIN is great with Miqo, even if you’re only very slightly hands-on with Miqo (like Bunshins) and don’t go all out to optimize, you’ll still be doing more DPS than 90% of the endgame playerbase. While I have done Savage with a lot of jobs with Miqo to test them out and play with them, Ninja is not one of them, so I don’t know how she will function in that environment, but as Ninja is less positionally dependent as DRG and MNK* I can’t see Miqo performing poorly in Savage content unless the player doesn’t understand the job/role well enough to help her out.
*in some fights positionals for MNK are simply nonexistent if you’re paying attention enough to use Riddle of Earth at every opportunity.