I got $\frac{q^{(n-k)}(q^{k+1}-1)}{q-1}$ for the total number of $X$ where I also included $X = V$. So if you want to count only the proper subspaces $X$ of $V$ you have to substract 1 from the above number.
My strategy is the following. First of all w.l.o.g. we can assume that $W$ is the spanned by $e_1,e_2,\cdots,e_k$, where $e_1,\cdots,e_k,\cdots,e_n$ is a basis of $V$, which I am going to call the canonical basis of $V$. I am going to compute the number $N_r$ that you defined in your OP. To compute $N_r$ I consider the action of the linear group $GL(V)$ acting on subspaces. Let $GL(V)_W$ be the subgroup of $GL(V)$ that stabilize $W$. Namely, $g \in GL(V)_W$ iff $g(W) = W$.
Here is the important claim:
Let $X,Y$ two subspaces of the same dimension such that $X + W = Y + W = V$ and $\dim(X \cap W) = \dim(Y \cap W)$ then there is $g \in GL(V)_W$ such that $$g(X) = Y$$
I leave to you the proof of the claim.
Then $N_r = \frac{\# GL(V)_W}{\# E_r}$ where $E_r \subset GL(V)_W$ is the subgroup which stabilizes a concrete $X_r$ e.g. $X_r$ spanned by $e_1,\cdots,e_r,e_{k+1},\cdots,e_n$. Now $g \in GL(V)_W$ iff its block matrix w.r.t. the canonical basis is $$g = \left( \begin{array}{cc}
A & C \\
0 & B \\ \end{array} \right) $$
where $A \in GL(\mathbb{F}_q^k), B \in GL(\mathbb{F}_q^{n-k})$ and $C \in \mathbb{F}^{k,n-k}$. If $g$ belongs to $E_r$ then the matrix $C$ must have the block form $$C = \left( \begin{array}{c}
E \\
0 \end{array} \right) $$
where $E \in \mathbb{F}^{r,n-k} $.
Then $N_r = \frac{\# GL(V)_W}{\# E_r} = \frac{\#GL(\mathbb{F}_q^k) . GL(\mathbb{F}_q^{n-k}). \# \mathbb{F}^{k,n-k}}{\#GL(\mathbb{F}_q^k) . GL(\mathbb{F}_q^{n-k}). \# \mathbb{F}^{r,n-k}} = q^{(n-k)(k-r)}$.
By summing these $N_r$ you get the total number I wrote above.
A concrete example: Let $V$ be a $4$ dimensional vector space over $Z_2$ and $W$ be a fixed $2$ dimensional subspace of $V$. Thus the possible dimensions of the complements of $W$ are $2$ and $3$. The number of $2$ dim. complements is $2^4=16$. (This matches with the count $N_0$ provided by you. Here $k=2,n=4,r=0,q=2$)
However, $N_1$= The no of 3 dim. complements of $W$= No of all $3$ dim. subspaces of $V$ - no of $3$ dim. subspaces of $V$ containing $W$ $=\binom{4}{3}_2−\binom{2}{1}_2=15−3=12$
– Angsuman Jun 25 '15 at 11:57