The following answer provide another, hopefully convincing, argument on why in category theory one can indentify isomorphic objects.
Categories of (multi-sorted) structures.
When dealing with categories of structures isomorphisms are bijective mapping preserving the structure. Basically this amounts saying that isomorphisms are ways to parametrize/rename the elements of one structure with names of another.
In this context changing the elements used for representing the structure does not change the structures, exactly like changing between decimal or hexadecimal basis does not change the structure of natural numbers. So isomorphic structures can and should be considered the same.
Also, when we fix the isomorphism we can identify elements of the two structures that are related by the isomorphism (but we have to keep track of the isomorphism considered, since different isomorphisms identify different pairs of elements).
With this little premise we can provide two reasons for why isomorphic objects should be considered the same in CT.
Philosophical reason.
One why to think about categories is to consider the objects as some abstract structures (like elements of a set can be thought as abstract points) and the morphisms as some abstract ways of relating them.
If we follow this point of view, and think category theory as a theory of abstract structures, then it should be natural to consider equal isomorphic objects, by abstaction of the structures' paradigm "isomorphic structures are the same".
Technical reason.
In this part we will make the previous argument formal but in order to do so we need a little premise on presheaves, also I will show an application of Yoneda Lemma which I consider particularly enlightening, so hold on and follow me.
A presheaf, on a category $\mathbf C$, is a functor $P \colon \mathbf C^\text{op} \to \mathbf{Set}$. You can think a presheaf as a multi-sorted algebra whose carriers are the sets $(P(c))_{c \in \mathbf C}$ and operations are the $(P(\sigma))_{x,y \in \mathbf C,\sigma \in \mathbf C[x,y]}$. Natural transformations are exactly homomorphisms for these algebras.
Now the yoneda embedding
$$ y \colon \mathbf C \to [\mathbf C^\text{op},\mathbf {Set}]$$
$$y(c) = \mathbf C[-,c]$$
provides an isomorphism between the category $\mathbf C$ (which as an algebraic structure) with a category of presheaves, namely the category of the presheaves of the representable presheaves.
From the discourse on isomorphisms of structures above we should think these two categories as being the same and we could identify (via the yoneda embedding) every object $c$ with the algebraic structure $y(c)=\mathbf C[-,c]$.
We now are ready to our final claim.
Let $c_1$ and $c_2$ be two isomorphic objects of $\mathbf C$. Clearly the algebras $\mathbf C[-,c_1]$ and $C[-,c_2]$ must be isomorphic as well.
Now putting together what we said in the beginning,
we can identify the $c_i$'s with their algebras, the $\mathbf C[-,c_i]$'s.
But since the $\mathbf C[-,c_i]$'s are isomorphic structures they should be regarded as the same, and so by a transitivity argument it should be natural to consider also $c_1$ and $c_2$ to be the same.
Hopefully this more practical argument will help you strenghten the belief that isomorphic objects can and should be considered the same.
I apologize for being so long, but I do not think I could have shorten this answer.