There are two things to note:
First: When you write
Store(A, x, y)
You create a term with three arguments , A, x, and y. There is no side-effect to A. You can create a name for this term by writing
B = Store(A,x,y)
Second: Z3 does not simplify terms unless you want it to. The python API exposes a simplification function called simplify. You can obtain the reduced term by calling the simplifier. The example is:
I = IntSort()
A = Array('A', I, I)
x = Int('x')
y = Int('y')
B = Store(A, x, y)
print Select(B,x)
print simplify (Select(B,x))