Personally, I found my ninja rely-ing on Isilla a lot. Mob up a bunch with that one Ninja Firewall and then North wind Spam stuff to oblivion. Isilla should proc a lot even with just 1 card effect, but I find the damage will still be lacking against stuff that's not weak to that particular element, though Rachel Sanc f1 and F2 still drop easy enough.
I'd drop the ALC cards in favor of Sapling carded Bradium Earrings (since you're a ninja, that'd be comparable to a Zerom carded orleans glove with a chance of auto-casting lvl 1 Improve conc when hit that for some reason also counts even when ciceda's blocking everything.) If you can, try to craft a
Keris with a +3 dex enchant and a drops card. If you can get +2% matk boost on that second enchant slot, you'd have a top tier weapon~
I can vouch for Scaraba's sorta, as my ninja is my main method of hunting 1-horn scaraba's for the imperial spears. With that ninja firewall and dragon fire, it can take anywhere from 4-6 casts of the dragonfire with like 80-ish int. If you do like to use dragonfire over the North wind method, due to the fact that one skill has delay, I'd focus more on +Int gear or +Matk vrs race cards in an Ashura [3]. Make those pop shots count for something. I've carded 3 Pinguicula cards in my ashura and the 1-horn scaraba's don't really pose too much threat now =x
In terms of higher tier magics on ninja, Dragon Fire Formation is probably the biggest burst damage you'll have in magic mode outside of maybe Ice spear. It does have a notable cooldown time, especially considering the other skills ninja has access to, so it's best to make use of that 5x5 cell splash damage to make up for that.
North Wind is the other Notable AoE on Ninja, as it's pretty much a Magical version of Snipers Sharp Shooting. It has a Strict 9 cell range at it's max level (From where you start casting, so if ciceda pushes you at all, the skill won't do anything and will still eat the wind stone). It has almost no cast delay at all, so if Isilla procs with it, you can spam it to your heart's content. I find it works incredibly well with crimson fire formation (especially with isilla gears) if the mobs elements will let it hit (I.E. snowiers are hit by fire, while ice titans will walk through and not be affected by it.) I leveled my ninja pretty reliably on Snow Harpies using this method. I dabbled a little bit in Ice dungeon 3, and things move slow enough if you have enough dex to solo there, though the Gazeti are as annoying as always.
I haven't found a use for the Ice meteor, it's freeze isn't guaranteed and you have to be right on top of the mobs. The Lightning jolt is fun, but Again, same style attack as Ice meteor without the status. It is spammable though.
Wind blade is horrendous, and needs a buff. It's slow, lvl 5 does about as much as lvl 3 Lightning bolt (From wind wings) with about the same cast delay), though lightning bolt costs less SP. Given the way the skill was set up, I'm guessing it was supposed to be like soul strike? But then they gave up halfway through and decided it needed a longer cast time.
Crimson fire blossom is nice that it's so spammable, but it's damage is low compared to skills like firebolt. Only base spell I'd consider maxing is the Ice spear.
[Important edit] Using lower levels of the base spells will let you cast them quicker, and thus help with the spammability. I've known ninja's who leveled well into the 90's using only lvl 1 Ice spear ad nauseum