This approach is completely reasonable, and is the obvious way of analyzing such a system. The equivalency can be show algebraically by expanding out the equation.
The simplest way of showing this is to use a Laplace-transform. If you are unfamiliar with this transform, the only thing you need to to follow this is that it is linear, it is written as $$\mathcal{L}\{u(t)\},$$ and it transforms derivation to multiplication with the variable s.
You have the equation
\begin{equation}
\frac{d}{dt}X = AX + B
\begin{bmatrix}
u_1(t)\\
u_2(t) \\
\end{bmatrix}
\end{equation}
Taking the Laplace-transform of each side yields
\begin{equation}
sX = AX + B
\begin{bmatrix}
\mathcal{L}\{u_1(t)\}\\
\mathcal{L}\{u_2(t)\} \\
\end{bmatrix}
\end{equation}
Manipulating this algebraically, we can show that
\begin{equation}
X = (s\mathbb{I}-A)^{-1}B
\begin{bmatrix}
\mathcal{L}\{u_1(t)\}\\
\mathcal{L}\{u_2(t)\} \\
\end{bmatrix} = h(s)\begin{bmatrix}
\mathcal{L}\{u_1(t)\}\\
\mathcal{L}\{u_2(t)\} \\
\end{bmatrix}
\end{equation}
(where the funky "I" represents the identity matrix,and I have collected all the matrices into one function, h(s), which is called the transfer-function).
From here, we can separate the input signals into their two frequency-components:
\begin{equation}
X = h(s)\begin{bmatrix}
\mathcal{L}\{c_1 \cos(w_1 t) + c_2 \cos(w_2 t)\} \\
\mathcal{L}\{d_2 \cos(w_1 t) + d_2 \ cos(w_2 t)\} \\
\end{bmatrix} =
\end{equation}
\begin{equation}
h(s)\begin{bmatrix}
\mathcal{L}\{c_1 \cos(w_1 t)\} \\
\mathcal{L}\{d_2 \cos(w_1 t)\} \\
\end{bmatrix}+ h(s)\begin{bmatrix}
\mathcal{L}\{c_2 \cos(w_2 t)\} \\
\mathcal{L}\{d_2 \ cos(w_2 t)\} \\
\end{bmatrix}
\end{equation}
Here we can see that X is now written as the sum of two parts:
\begin{equation}
X_1 = h(s)\begin{bmatrix}
\mathcal{L}\{c_1 \cos(w_1 t)\} \\
\mathcal{L}\{d_1 \ cos(w_1 t)\} \\
\end{bmatrix}
\end{equation}
\begin{equation}
X_2 = h(s)\begin{bmatrix}
\mathcal{L}\{c_2 \cos(w_2 t)\} \\
\mathcal{L}\{d_2 \ cos(w_2 t)\} \\
\end{bmatrix}
\end{equation}
Each of these can now be reverse-transformed back into the time-domain to give two systems that you can analyze separately:
\begin{equation}
X_n = h(s)
\begin{bmatrix}
\mathcal{L}\{c_n \cos(w_n t)\} \\
\mathcal{L}\{d_n \ cos(w_n t)\} \\
\end{bmatrix} = (s\mathbb{I}-A)^{-1}B
\begin{bmatrix}
\mathcal{L}\{c_n \cos(w_n t)\} \\
\mathcal{L}\{d_n \ cos(w_n t)\} \\
\end{bmatrix}
\end{equation}
\begin{equation}
\implies sX_n = AX_n + B
\begin{bmatrix}
\mathcal{L}\{c_n \cos(w_n t)\} \\
\mathcal{L}\{d_n \ cos(w_n t)\} \\
\end{bmatrix}
\end{equation}
\begin{equation}
\implies \frac{d}{dt}X_n = AX_n + B
\begin{bmatrix}
c_n \cos(w_n t) \\
d_n \ cos(w_n t) \\
\end{bmatrix},
\end{equation}
and we can see that this is identical to your proposed partitioning.