I am learning basics of the category theory (CT).
I do understand that CT is a modern powerful framework to describe various branches of mathematics in a unified way.
I do admit that category's definition tells a lot about the whole thing and focuses on the most important properties, shadowing unnecessary details. However, the more I go forward, the more it feels like it should explicitly require a notion of morphisms equality (like it does with morphism composition). It feels so because equality or inequality of morphisms arises everywhere, since the very beginning: any commutative diagram eventually reduces to an equality of two different paths and many other things involve equality as well. Even composition is defined grounding upon an (implicit) equality!
I'll try to give an example of my concern. Consider $\mathbb{SET}$. Its objects are sets and morphisms are functions. Now, let's recall that functions are sets as well - to be more precise, a function $f : A \mapsto B$ is a subset of a $A \times B$ obeying certain properties, which I omit. Thus, one could argue that $f$ is both a morphism between objects $A, B \in Obj(\mathbb{SET})$ and an object defined as a set of pairs $\{ (a_1 \in A, b_1 \in B), ..., (a_n \in A, b_n \in B) \}$ and those are equal because both are essentially exactly the same thing.
I hope my concern is clear and I need some kind of "conceptual insight" from knowledgeable people to move forward. Please give me the right perspective.
Morphism equality is indeed taken as primitive, but at an "even more primitive" level than composition.
Remember - ignoring set/class issues for the moment - composition consists of a partial function assigning to a pair of morphisms (on which it's defined) a third morphism, which we call their composition. So equality between morphisms is folded into the very nature of sets themselves (in this case, the sets of morphisms).
If you're familiar with model theory, equality is part of the logical language - on the same level as the quantifiers and Boolean connectives - while compositionof morphisms would be part of the signature (or language, or vocabulary, or ...), similarly to the symbol for the group operation in the context of groups.
Your second-to-last paragraph, though, is more special. The phenomenon you're describing there is actually something category theory explicitly doesn't want to pay attention to, at least most of the time, since one of the big points is that we can forget what the objects are and just look at how the morphisms behave. Certainly there's no object/morphism relation in general categories - for example, think about a group viewed as a one-object category.