We obviously use three independent keys. The security of the composition is then at least as good as the security of the best of these algorithms. (You're right that it's not much better, but it doesn't need to be; I don't see how you get "much less", were you thinking of using the same key for each algorithm?)
If you somehow convince yourself that the NSA can break many well-known encryption algorithms and that it's willing to risk exposing this ability to shut down your botnet (which is the counterfactual I'm working off in this thread), this may give you some peace of mind: Blowfish and AES are well-tested designs by separate teams and SALSA is a very simple, very different design that you can easily implement yourself and that's pretty resistant to side-channel attacks. It seems likely that any agency that can break all three can break anything you can come up with.
