Let's consider the following complex number: $z= 3+2i$, then you calculate $r (\arg z)$ by: $r=\sqrt {3^2+2^2}=\sqrt {13}$
But why don't you use this calculation: r=$\sqrt {3^2+(2i)^2}=\sqrt {3^2+4i^2}=\sqrt {9-4}=\sqrt{5}$?
Isn't the "height" $2i$, which is an imaginary number? Why can you simply convert it to a real number "$2$"?

No, its height is $2$, the real part of $2i$. $i$ has no height. We are moving $2$ units on the imaginary axis with $2i$.
The $i$ tells us we're on the imaginary plane, and that's just how we plot it on the imaginary plane. Applying the Pythagorean theorem to complex numbers, their magnitude, or distance from the origin, is the square root of the sum of the squares of the real parts.