Oh no, that's a lot, you're not using sprite atlas definitely. I've got 20 set pass calls on a screen full of prefabs.
I recommend you this packer, it's simple to use and efficient:
https://www.assetstore.unity3d.com/en/#!/content/12976Use collisions for collisions, as the name states, use trigger for flythrough stuff, like bullets passing through multiple enemies.
I haven't used Pooler so i don't know how it fares compared to Pool Boss, but the cool thing about Core Game Kit is that it integrates pooling, spawning and my favourite, the killable module which you can use for defining attack/hit points, ignoring offscreen hits, invincibility settings, layer and tag filters, death timers, death prefabs, death variable modifiers and a lot more.
Unibullet hell also has the possibility to spawn bullets from the Pool Boss pool. It works great with Playmaker, let me know if you need any advice, i couldn't imagine making a shmup without these tools.