OK, now this is a topic that might not appeal to everyone, but I am very interested in the metaphysics of fantasy worlds. I blame Torg, back in the early 1990s, for igniting this interest, but that's long in the past now (though find the right mailing list and the debates still rage!)
Anyway, the metaphysics of warhammer world are something of a mixed bag. In two areas, they are relatively clear. Magic definitely exists, we know (roughly) what powers it, where it comes from and how different types of magic user manipulate it. We also have some understanding of the relationship between Magic and the other area where the metaphysics are reasonable clear: Chaos. We know Chaos is something that comes from another dimension or realm, we know that the Chaos Gods are real and have something akin to physical form, even if we don't know if they are corporeal in the sense of being able to manifest directly in Warhammer World. We know from their daemon servants that they are entities, not metaphysical concepts, albeit cosmically powerful entities that would make all but the most powerful denizens of superhero universes shrink in fear.
But Gods, now the Gods I'm not clear on. We do know that Invocations are real. It is possible for the faithful to bring about miraculous effects, and the effects that they can invoke are strictly limited according to the God (or Gods?) that they have primarily focused their faith upon. However, it would appear that the difficulty of an invocation isn't based on how powerful an individual god is or how strong its following, but has some relative objectivity about it (and ignore for a moment the fact that this is because of game balance - game balance may be the fundamental design motivation, but the reason should be found within the metaphysics). We also know that gods can go in and out of favour, but this doesn't seem to affect the ability of the faithful to call down miracles in their name. And we also know that it is possible for a mortal to become a God (Sigmar, the dwarven gods, and possibly Myrmidia).
However, what we don't know is something more fundamental - are the gods real? Real, in the same sense as the chaos gods, in that they have a separate objective existence regardless of the belief of their followers, with their own personal and unique motivations. I have a feeling that they may not be. There is a clear hint in the WFRP3 core set (maybe in the Tome of Blessings?) that invocations may simply be a different way of accessing the winds of magic - this doesn't mean that a diety isn't involved of course, because the power path may be "Invoker -> Diety -> Magic -> Diety -> Invoker". There is also talk of gods being subsumed within other gods, so that where once Rhylla was one of the eldest, fundamental dieties, now she is considered an aspect of Taal. This implies that the gods may not, therefore, be distinct entities. And finally, there seem to be some strong contrasts between the chaos dieties and the gods of faith - the Gods do not directly bestow blessings in the form of positive mutations or marks; the Gods do not seem to have armies of angels / valkyries / whatever to fight against the daemon hordes; and the Gods appear to act through the churches of their formal religions, not by identifying susceptible individuals and empowering them to spread the word of the true faith.
It seems to me that much of the evidence seems to point to a belief-based model of godhood - if enough people believe (or a single person believes strongly enough), they can invoke miracles based on that belief - that Faith. The next question is, assuming this is the case, does that Faith make the belief come true (enough people believe that Sigmar ascended to godhead, so he did) or is there in fact no middle man at all, none of the gods exist, and they are just handy labels for the known faiths against which the pious invoke miracles.
Personally, I hate this model. It's great the way Terry Pratchett uses it, as an ironic device, but within a "serious" fantasy world it has a scientific-rationalist feel about it that doesn't feel like it belongs alongside the forces of chaos and magic. I think a fantasy world is more interesting if the gods are real - the Graeco-Roman model of the interefering, all-too-human dieties who do genuinely need to be appeased, because they have fears, desires and motivations themselves and you better keep them sweet or one day they might just turn spiteful.
I'll end now. From what I've seen and read, the metaphysics aren't conclusive on this point. And there's always the argument that "God is Real" and "God is Real because people believe" is indistinguisable in the time span of pretty much any roleplaying campaign. But these things interest me: Warhammer World is just one of many possible cosms in the Torgian infiniverse, and I want to know what sort of cosm it is!