The concepts of gods exists, but their existence is left an open-ended question, particularly with regards to the Sovereigns and Six, the most commonly worshiped pantheon in Eberron. The following excerpt from this blog post Keith wrote, while not technically "canon" in the strictest sense, explains the mentality and concepts that most people on Eberron hold towards the gods:
Dark Six: Myths and The Fury
There are many myths of the Sovereigns and Six. Dol Arrah battling Death itself. The Mockery’s betrayal of his siblings Dol Arrah and Dol Dorn, only to be stripped of name and skin by his brother. The Keeper bargaining with Death to gain the power to steal souls. The birth of the Fury, Aureon unleashing the Shadow. We’ve only mentioned a few of these myths in canon sources, but there are hundreds within the world. Often these explain natural phenomena; the massive volcano in the Mror Holds is called the Fist of Onatar, because it’s said that Onatar smashed the mountain to create his first forge.
How can this be? Deities don’t physically manifest in Eberron. The Devourer is the storm and the raging sea, not an angry giant who’s going to personally knock your house down. The answer is that the myths are tales of their deeds before they became the Sovereigns. Reality was created by the struggle between the Progenitors. Khyber’s children rose from the darkness and seized control of the world. A band of heroes rose in this time to battle the fiends and establish the foundation for civilization. The myths are the stories of these champions… heroic deeds, vile betrayals, and more. Ultimately these champions defeated the Overlords. This left the world in need of guiding hands: and so these first heroes and villains ascended to become the Sovereigns and Six, merging with reality and rising to a higher form of existence. So there are many tales of Dol Arrah’s heroism, but no one expects her to physically manifest today; vassals know that she is ALWAYS with them, guiding the hand of every virtuous warrior.
There’s no canon list of these myths, in part because there are many different interpretations across different cultures. The common vassal traditions of the Five Nations are based on the Pyrinean Creed, developed in Sarlona before Lhazaar’s journey. But the Talentans say Bally-Nur was a clever halfling hunter, and if you go to Khazaak Draal you’ll hear stories about the Shadow never told in a human temple. The Church of the Wyrm Ascendant is a sect in the Five Nations that claims that the Sovereigns were dragons, and that the myths are based on the actual deeds of draconic champions and villains in the Age of Demons. However, this isn’t a universally accepted belief. Most myths are vague about the nature of the Sovereigns, and it’s common for them to be depicted as members of the dominant culture sharing the story. Pyrinean temples occasionally depict the Sovereigns as dragons, but this is considered to be metaphor, not literal portraits.
The point is that while the Sovereigns and Six don’t manifest in the world and can’t be proven to exist, you CAN have artifacts, locations, or deeds that are attributed to them. You can visit the Lair of the Keeper, or find Dol Arrah’s Sunblade
or a cloak said to be made from the flayed skin of the Mockery. That doesn’t mean these things are actually what people say they are—but the idea of finding Dol Arrah’s sword isn’t at odds with her never manifesting today, because this was her sword before her ascension.
Of course, this doesn't apply to those who follow the Undying Court or the Cults of the Dragon Below, whose patrons can be shown to exist -- you can go into Aerenal and speak with the Undying Court, or descend into Khyber to confront the daelkyr (though you would have to be very brave and/or stupid to do so). This also doesn't apply to the Blood of Vol, the Path of Light, and the Druidic traditions of Eberron. The Blood of Vol puts no faith in the gods, and those Seekers that do believe that they exist denounce them as cruel tyrants. The Path of Light is primarily a philosophy rather than a religion; the kalashtar do "worship" il-Yannah, but as a force of compassion and courage, not as a concrete deity. And the Druids of Eberron believe they draw power from the world itself.