With a main tool is signed graphs, we give a full description of the characteristic quasi-polynomials of ideals of classical root systems ($ABCD$) with respect to the integer and root lattices. As a result, we obtain a full description of the characteristic polynomials of the toric arrangements defined by these ideals. As an application, we provide a combinatorial verification to the fact that the characteristic polynomial of every ideal subarrangement factors over the dual partition of the ideal in the classical cases.