I've spent way too much time working on this, but I think I've more or less figured out the Eilira fight on hard difficulty, getting to probably something around an 80-90% win rate (the 26000 HP/2600 attack master with harpies where the story continues even if you lose).. though, I am pretty overleveled and at a lower level the win rate would obviously be somewhat lower. There are a few key factors to this fight that you can (ab)use to be able to beat it much more consistently:
1) When her board is full of 3 traps/spells, she becomes way less dangerous - try to avoid triggering or destroying her traps at almost any cost. When she can't cast spells, she can't trigger her abilities very often, and she can't summon more than 1 monster per turn. It's pretty easy to kill 1 harpy per turn, and she also only has 6 regular harpies in her deck.. so once you put her in this position you've usually won.
2) When her board is already full of traps/spells, make sure that you have no traps left, again, at almost any cost. If you have no traps on your board, then she can't discard cards with her harpies, which both prevents her from triggering her trap that draws her more cards and prevents her from discarding the card that summons more stuff to the board on discard. 1 Harpy at a time can easily be killed by the ninjas, but multiple harpies can get messy fast.
3) Her trap that draws cards when a wind effect/spell/trap is activated - you should treat this as a countdown to losing the game. If she draws 3 cards from it, you've almost certainly lost. The card draw in itself wouldn't necessarily be the end of the world, but where it really goes wrong is that once it's destroyed she can special summon her 6 star harpy (or even 2 of them) and everything tends to go quickly downhill from there. It's not impossible to recover.. but it's pretty difficult, and you should really try to avoid being put in that position in the first place if at all possible.
Anyway, the deck - ideally, you never cast spells after the first turn unless you're desperate (card draw and deck thinning pretty much to try to get your ninjas as consistently as possible), and never try to play the mirror shields (so she can't trigger her traps and can't discard cards to destroy the mirror shields). The mirror shields are an absolute last resort, not something that you plan to play - additionally, if you absolutely have to use the mirror shields, then be sure to use *all* of them (ie. play 2-3 mirror shields, and then no matter what happens you spend all of them that turn even if it means using an extra one to do nothing - it's better to have 0 traps than 1 trap.. it might sound dumb to spend a mirror shield and discard a card to do nothing, but trust me, I've learned that from experience). Obviously, when you have multiple ninjas of the same type, try to ensure that they're the ones that are left on the board at the end of a turn so you always have 1 of each ninja.
Initially you don't want to put your monsters in defense mode, but once she stops playing monsters you'll want to start putting them in defense mode to keep them alive if you're short on monsters, and you can sometimes use the pirates as chump blockers too depending on the situation (early on you may want to discard them, but once you're in the winning position where her spells are all blocked then you're never going to play any cards to discard the pirates anymore so they're just completely expendable at that point). Also, it's almost always better to kill a monster with your master than it is to have a damaged monster at the end of a turn, even if that means putting your hero down to very low health (and don't even think about leaving enemies alive if you have a choice - even if you go down to 1 HP it's better to kill the enemy). Oh, also, when one of your ninjas becomes wind type, be sure to play them at the start of a turn rather than using their ability to avoid triggering nasty effects (when you return them to your hand they'll become dark type again).