Okay, I've given this matter some thought and the connection I think you're seeing is "there isn't anything there" applies to both the idea of vacuum (bottled nothingness) and atheism (there isn't any God). Is this correct or are you thinking of some other connection between the arguments? If not, you'll have to elucidate the similarities you see.
Not exactly, but your second paragraph comes close enough to understanding what I'm getting at that I almost don't need to explain any better.
I guess the connection I see, though, isn't so much specific to the case of the vacuum as to knowledge in general. The claim that there is a god is to me no different from any other claim. The question is whether or not it is more difficult to test.
I don't think it necessarily is. The point Hobbes is making (or at least the point Zimmer attributes to him, it doesn't really matter for our sake whether he made it or not) seems to be that experiment is useless because there's always some other hypothesis that can account for your results.
The point I think that you're making with god is that experiments that seek to find whether god exists are useless because there's always some hypothesis under which we can still fit a god in to the universe. God is in the gaps that we haven't or can't look at, or maybe has no effects at all.
If that is what you are thinking of then I don't think the two are similar because one is dealing with knowledge gained from experimentation and other hypotheses can be eliminated by testing for differences between what the various hypotheses predict.
The problem here is that once you've tested a hypothesis and it's come up wanting, you can always change it in a way that would allow it to still fit the data.
Maybe always is too strong, but I think it's pretty close to accurate.
Regardless, it's still always true that there will be some other hypothesis that could easily be dreamed up that would fit all the experimental results.
I don't think you can experimentally test the hypothesis of "no God" versus "a non-material God that does not physically affect our reality".
Ah! I've been having a hard time making myself clear until now, but I think this helps. What I'm saying is that yes, you can't experimentally test to see which of those is true - but the same will be true of any scientific claim - there will always be an alternative hypothesis which is not compatible with the one you've tentatively accepted based on the experiment, but which you also won't be able to eliminate based on your experimental data, or in fact any future experiments. I think that's basically the point Hobbes was making, and I think your point here is only a special case of it.
So the question becomes "How do we choose between two different hypotheses when both are consistent with experiment?"
Edit: This question is not specific to the issue of god, but is one that science faces (and deals with quite well I think) every day.