I wanted to address the general question without getting into your specific examples of which beliefs require accepting irrationality.
G-d is infinite and we are finite. The most basic thing that we can understand about G-d is that He is beyond our understanding. The Rambam writes in several places (Hilchos Teshuva, Moreh Nevochim part 3) that G-d's "knowledge" is not in the same realm as our knowledge, and we cannot comprehend what G-d's knowledge is. Even the fact that G-d is unlimited is not a description of essence, but just an expression of the fact that we cannot assign any definitions (Vilna Gaon's explanation of אין סוף).
I once heard R' Yaakov Weinberg explain that this is a function of G-d's existence being absolute while the existence of everything else is not (Rambam Yesodei Hatorah 1:1-5 and 1st Ikkar). Thus, this state is inherent in the nature of existence, and not merely something G-d held back from us.
That being the case, there will obviously be some things that we cannot grasp, because they are beyond the faculties of human knowledge to grasp, and a person only understands what he can experience (Derech Hashem 1:1:5). The infinite is beyond our grasp, and how an infinite Being could create or relate to a finite creation is also beyond our grasp, and there will therefore be parts of existence which are inherently incomprehensible to us.