A question: I'm statting up an opponent (an NPC runner) with the chem-gland/weapon reservoir poison blade setup, using Gamma-Scopolamine from the core book. From the flavor, it looks like it's essentially the muscle relaxer from hell. So my question is, how likely is this to paralyze someone with Muscle Replacement? Is enough of the structure replaced with mechanical elements as to prevent the paralysis?

Short answer: No, unless specifically stated there is not side benefit prevent paralysis.

Bit longer and inherently biased answer: That would be an actual side benefit to augmentation which with the games pro-magic bias they'd never do.

I think scopolamine acts on the nervous system, not the muscles.

It does indeed. However, it would be hard to replace muscles without also replacing the peripheral nerves (or at least nerve endings) that control them.
Scopalimine also has effects on (the nerves controlling) smooth muscle tissue, which is stuff like the muscles in your organs. Muscle replacement wouldn't affect those muscles, so you'd still get a lot of nasty effects.

By RAW, it has no effect. As a house rule, it might be cool to say that folks with muscle replacement get bonus dice to resist certain things, like drugs that cause paralysis and even the secondary effects of electrical shock. Gives people a reason to actually use muscle replacement instead of the muscle toner / augmentation.

Why would they? Even the muscle replacements are still following the command of the nervous system. If the required transmitters are blocked, no signals reach the muscle replacement. There is no plausible reason as to why they should get a bonus. None.

hrm. well, i think that actual cyber-replacements would be even better for this, then. lets face it, some of things are even wired as drones (such as modular hands), so if you cant move your meat limbs, you should still have DNI for your metal limbs. and if it is nerve based, wired reflexes would probably help a lot.

muscle replacement would make drugs that you inject into muscles a bit more strange i suspect.

Yeah, I kind of figured a full cyberlimb would be essentially immune, although maybe that's not the case if there's a nerve element as well to its effects. But I guess I just wasn't sure how much gets actually replaced in muscle replacement. It sounds like the consensus is that there's enough biological elements left that it should have some effect at least? Thanks for the comments guys.

It would depend on where the drug was administered. If it were administered into the regular bloodstream, it would still fully affect the cyberlimb.