I'll go point by point with you because I really quite liked both S9 arcs and people shit on them too frequently for my tastes.

I just don't believe that there's any way that any force on Earth Bet could hope to win against several hundred full-powered clones of some of the strongest and most insane parahumans who ever lived.

Recall that the Undersiders privately discussed how the S9 were basically them, but stronger and murderous; they are most successful when they ambush and otherwise set the rules of engagement. Apart from the Siberian, Jack Slash, Bonesaw, Grey Boy, and Crawler, none of them are particularly difficult to kill if the tables are turned - this is why they're always going around to look for new members.

Yes, it's grossly unfair, but for all but Bonesaw and Jack Slash they already know the tricks required to kill the fuckers, and that's really all they need.

I mean, 1 Siberian was bad enough, but 9 at once is just too ludicrous to believe. And those 9 Siberians are only a tiny fraction of the Slughterhouse's cloned power.

The Siberian is only invincible prior to learning about Manton. After that Siberian becomes nothing more than an extremely dangerous enemy as opposed to a mobile Act of God. The same can be expressed with all the other ones - Crawler isn't so bad when you know you have to hit him hard enough to kill him all over, Cherish isn't so bad when you know you need to use proper Master/Stranger protocols and know that stealth isn't going to be a thing, Hatchet Face isn't really a problem if you hit him from outside his range, etc. The S9 clones are bad, but the worst thing about the originals was the mystery.

And speaking of clones, could someone please explain how Blasto's cloning tech can clone powers? I was under the impression that the powers come from the passenger, which doesn't live in this universe. How did the passenger get cloned along with the person?

The passengers aren't terribly aware of the differences between humans. Note how Fenja and Menja had identical powers because they were identical twins - the passenger likely thought that they were copies and as such they both got the same power. In this case Bonesaw uses Blasto's tech to clone the bodies and Cranial's tech to tweak the memories so that they're similar enough to the original for the passenger to think "Oh, there's my host. A whole bunch of it, what fun." Generally speaking Tinkertech is bullshit and trying to demarcate what it can and can't do is a fool's errand, but in this case the logic follows.

I want to finish reading Worm, because I want to know where it eventually leads. I really like Taylor, and I want to know what happens with Dragon/Defiant, the Endbringers, the source of power, etx. But both of the Slughterhouse Nine arcs have left my suspension of disbelief in tatters, and I just can't bring myself to continue without a serious repair job.

Hope this helped.

Tl;dr version: The S9 are scary but primarily when they're on the attack and here they're on the defence; the biggest advantage the S9 had was secrecy and they don't have it anymore; passengers are kind of dumb; Tinkertech is bullshit and Bonesaw is particularly advanced bullshit.