Let me present another approach to this interesting problem, which will allow to get a closed expression for $N(m,k,q)$.
Let's consider a word of length $m$ from the binary alphabet $\{0,X\}$, having a total of $s$ zero's.
$$
\begin{array}{*{20}c}
X &| & {0,} & {0,} & {0,} &| & X &| & 0 &| & {X,} & X &| & {0,} & 0 &| & X \\
0 &| & {1,} & {2,} & {3,} &| & 0 &| & 1 &| & {0,} & {0,} &| & {1,} & 2 &| & 0 \\
\end{array}
$$
Imagine to sequentially scan the word and count the number of consecutive zeros, resetting the counter
when the character is different from $0$, as in the exaple above.
Then we can bi-ject each word with an hystogram which has :
- $j$ bars;
- sum of the bars equal $s$;
- $m-s$ Xs.
Now, the number of ways to compose $j$ bars, summing to $s$, and with a heigth going
from $1$ to max $r$ is given by
$$
N_b (s - j,r - 1,j) = \text{No}\text{.}\,\text{of}\,\text{solutions}\,\text{to}\;\left\{ \begin{gathered}
\text{0} \leqslant \text{integer}\;x_{\,j} \leqslant r - 1 \hfill \\
x_{\,1} + x_{\,2} + \; \cdots \; + x_{\,j} = s - j \hfill \\
\end{gathered} \right.
$$
which is expressed by
$$ \bbox[lightyellow] {
\begin{gathered}
N_b (s - j,r - 1,j)\quad \left| \begin{gathered}
\;1 \leqslant \text{integer }r \hfill \\
\;0 \leqslant \text{integer}\;j \leqslant \text{integer }s \hfill \\
\end{gathered} \right.\quad = \hfill \\
= \sum\limits_{\left( {0\, \leqslant } \right)\,\,k\,\,\left( { \leqslant \,\frac{{s - j}}
{{r - 1}}\, \leqslant \,j} \right)} {\left( { - 1} \right)^k \left( \begin{gathered}
j \hfill \\
k \hfill \\
\end{gathered} \right)\left( \begin{gathered}
s - 1 - k\,r \\
s - j - k\,r \\
\end{gathered} \right)} \hfill \\
\end{gathered}
\tag{1} }$$
as explained in this post.
Then we can dispose the $m-s$ (undistinguishable) X place-holders and the $j$ (distinguishable) bars by
- reserving $j-1$ X's as separators between consecutive $0$ blocks
- putting the remaining X's in any of the $j+1$ interstices, thus in ${m-s+1} \choose{j}$ ways.
Finally we can compose the Xs in $(q-1)^{m-s}$ ways.
We shall pay attention to that $j \leqslant s \leqslant \left\lceil {m/2} \right\rceil $
Thus the Number sought for, understood as
the number of words which contains max $k-1$ consecutive zeros (in one or more runs) will be
$$
\eqalign{
& N(m,k,q)\quad \left| \matrix{
\;1 \le {\rm integer }k,q \hfill \cr
\;0 \le {\rm integer}\;m \hfill \cr} \right.\quad = \cr
& = \sum\limits_{0\, \le \,\,s\,\, \le \,m} {\left( {q - 1} \right)^{\,m - s} \sum\limits_{0\, \le \,\,j\,\, \le \,s} {\left( \matrix{
m - s + 1 \cr
j \cr} \right)\sum\limits_{\left( {0\, \le } \right)\,\,i\,\,\left( {\, \le \,j} \right)} {\left( { - 1} \right)^i \left( \matrix{
j \cr
i \cr} \right)\left( \matrix{
s - 1 - i\,\left( {k - 1} \right) \cr
s - j - i\,\left( {k - 1} \right) \cr} \right)} } } = \cr
& = \sum\limits_{0\, \le \,\,s\,\, \le \,m} {\left( \matrix{
\left( {q - 1} \right)^{\,m - s} \quad \cdot \hfill \cr
\sum\limits_{\left( {0\, \le } \right)\,\,i\,\,\left( {\, \le \,m - s + 1} \right)} {\left( { - 1} \right)^i \left( \matrix{
m - s + 1 \cr
i \cr} \right)\sum\limits_{\left( {0\, \le } \right)\,\,j - i\,\,\left( { \le \,s - i} \right)} {\left( \matrix{
m - s + 1 - i \cr
j - i \cr} \right)\left( \matrix{
s - 1 - i\,\left( {k - 1} \right) \cr
s - i\,k - \left( {j - i} \right) \cr} \right)} } \hfill \cr} \right)} = \cr
& = \sum\limits_{0\, \le \,\,s\,\, \le \,m} {\left( {q - 1} \right)^{\,m - s} \sum\limits_{\left( {0\, \le } \right)\,\,i\,\,\left( {\, \le \,m - s + 1} \right)} {\left( { - 1} \right)^i \left( \matrix{
m - s + 1 \cr
i \cr} \right)\left( \matrix{
m - i\,k \cr
s - i\,k \cr} \right)} } = \cr
& = \sum\limits_{0\, \le \,\,s\,\, \le \,m} {\left( {q - 1} \right)^{\,m - s} \sum\limits_{\left( {0\, \le } \right)\,\,i\,\,\, \le \,m/k} {\left( { - 1} \right)^i \left( \matrix{
m - s + 1 \cr
i \cr} \right)\left( \matrix{
m - i\,k \cr
m - s \cr} \right)} } = \cr
& = \sum\limits_{\left( {0\, \le } \right)\,\,i\,\,\, \le \,m/k} {\left( { - 1} \right)^{\,i} \sum\limits_{0\, \le \,\,m - s\,\, \le \,m} {\left( \matrix{
m - i\,k \cr
m - s \cr} \right)\left( {\left( \matrix{
m - s \cr
i \cr} \right) + \left( \matrix{
m - s \cr
i - 1 \cr} \right)} \right)\left( {q - 1} \right)^{\,m - s} } } = \cr
& = \sum\limits_{\left( {0\, \le } \right)\,\,i\,\,\, \le \,m/k} {\left( { - 1} \right)^{\,i} \left( {\left( \matrix{
m - i\,k \cr
i \cr} \right)q^{\,m - i\,k - i} \left( {q - 1} \right)^{\,i} + \left( \matrix{
m - i\,k \cr
i - 1 \cr} \right)q^{\,m - i\,k - i + 1} \left( {q - 1} \right)^{\,i - 1} } \right)} = \cr
& = q^{\,m} \sum\limits_{\left( {0\, \le } \right)\,\,i\,\,\, \le \,m/k} {\left( {\left( \matrix{
m - i\,k \cr
i \cr} \right)\left( {{{1 - q} \over {q^{\,k + 1} }}} \right)^{\,i} } \right)} - q^{\,m - k} \sum\limits_{\left( {0\, \le } \right)\,\,i\,\,\, \le \,\left( {m - k} \right)/k} {\left( {\left( \matrix{
m - k - i\,k \cr
i \cr} \right)\left( {{{1 - q} \over {q^{\,k + 1} }}} \right)^{\,i} } \right)} = \cr
& = q^{\,m} \sum\limits_{\left( {0\, \le } \right)\,\,i\,\,\left( {\, \le \,m/k} \right)} {\left( {\left( \matrix{
m - i\,k \cr
m - i\,\left( {k + 1} \right) \cr} \right)\left( {{{1 - q} \over {q^{\,r + 1} }}} \right)^{\,i} } \right)} - q^{\,\left( {m - k} \right)} \sum\limits_{\left( {0\, \le } \right)\,\,i\,\,\,\left( { \le \,\left( {m - k} \right)/k} \right)} {\left( {\left( \matrix{
\left( {m - k} \right) - i\,k \cr
\left( {m - k} \right) - i\,\left( {k + 1} \right) \cr} \right)\left( {{{1 - q} \over {q^{\,k + 1} }}} \right)^{\,i} } \right)} = \cr
& = M(m,\;k,\;q) - M(m - k,\;k,\;q) \cr}
$$
where:
- in the first passage we use the trinomial revision $\left( \matrix{ s \cr j \cr} \right)\left( \matrix{ j \cr n \cr} \right) = \left( \matrix{ s \cr n \cr} \right)\left( \matrix{ s - n \cr j - n \cr} \right)$
- in the sum in $s$ we use $\sum\limits_k {\left( \matrix{ n \cr k \cr} \right)\left( \matrix{ k \cr m \cr} \right)y^{\,k} } = \left( \matrix{ n \cr m \cr} \right)\left( {1 + y} \right)^{\,n - m} y^{\,m} $
obtainable from
$$
\left( {1 + y + y} \right)^{\,n} = \sum\limits_{\left( {0\, \le } \right)\,\,k\,\,\left( {\, \le \,n} \right)} {\left( \matrix{
n \cr
k \cr} \right)\left( {1 + y} \right)^{\,k} y^{\,n - k} } = \sum\limits_{\left( {0\, \le } \right)\,\,k\,\,\left( {\, \le \,n} \right)} {\sum\limits_{\left( {0\, \le } \right)\,\,j\,\,\left( {\, \le \,n} \right)} {\left( \matrix{
n \cr
k \cr} \right)\left( \matrix{
k \cr
j \cr} \right)y^{\,n - j} } }
$$
In conclusion
$$ \bbox[lightyellow] {
\left\{ \matrix{
M(m,k,q) = q^{\,m} \sum\limits_{\left( {0\, \le } \right)\,\,i\,\,\left( {\, \le \,m/k} \right)} {\left( {\left( \matrix{
m - i\,k \cr
m - i\,\left( {k + 1} \right) \cr} \right)\left( {{{1 - q} \over {q^{\,k + 1} }}} \right)^{\,i} } \right)} \hfill \cr
N(m,k,q) = M(m,\;k,\;q) - M(m - k,\;k,\;q) \hfill \cr} \right.\quad \left| \matrix{
\;1 \le {\rm integer }k,q \hfill \cr
\;0 \le {\rm integer}\;m \hfill \cr} \right.
\tag{2} }$$
and it can be verified that the above expression
- ${\bbox[#dfd,5px]{\text{satisfies the recursion provided in *N. Shales*'s answer}}}$
- ${\bbox[#dfd,5px]{\text{gives the terms of the z-transform provided in *Markus Scheuer*'s answer}}}$ .