John describes his impression of the empty tomb as something that brought him belief but without understanding. His faith was well grounded in evidence, not simply in word of mouth or feelings, yet it didn't require him to understand in order to believe. Sometimes God chooses not to give us all we need in order to understand but chooses instead to give us just enough to believe and to trust in Him. The details will come later, when we need them. Until then it is enough to believe. It is enough to realize that He is not dead, though He very clearly did die. The implications of that miracle and the full understanding of what He is now will come later.