Your conjecture is true. Here is a proof.
Define $\operatorname{Av}_n(w)$ to be the number of binary words of length $n$ which avoid the pattern $w$.
Let $u$ and $v$ be binary words with $|u| = k$ and $|v|=m$ with $k < m$. We will show that $\operatorname{Av}_n(u) < \operatorname{Av}_n(v)$ for all $n$.
Define the special words $$M_n = \overbrace{00\cdots00}^n\qquad\text{and}\qquad L_n = \overbrace{00\cdots01}^n.$$
We can show fairly easily using the cluster method of Goulden and Jackson (and other ways as well, though the cluster method works easily for any pattern) that words avoiding $M_n$ and words avoiding $L_n$ have the generating functions $$m_n(x) = \sum_{r \geq 0}\operatorname{Av}_r(M_n)x^r = \frac{1-x^n}{1-2x+x^{n+1}}$$ and $$\ell_n(x) = \sum_{r\geq 0} \operatorname{Av}_r(L_n)x^r = \frac{1}{1-2x+x^n}.$$
Moreover, of all words $w$ with $|w|=n$, $M_n$ is the most avoided word and $L_n$ is the least avoided word. Formally, for $w$ with $|w|=n$ and all $r$ $$\operatorname{Av}_r(L_n) \leq \operatorname{Av}_r(w) \leq \operatorname{Av}_r(M_n).$$
This can be seen probabilistically by observing that the number of occurrences of a pattern of length $n$ in all words of length $r$ is independent of what the pattern is. Since $M_n$ "packs" the most easily (i.e., has a lot of overlaps) and $L_n$ does not "pack" at all (i.e., cannot overlap itself), it follows that $M_n$ appears as a pattern in less words overall than any other pattern and $L_n$ appears as a pattern in more words overall than any other pattern.
It should also be obvious that $\operatorname{Av}_r(L_n) \leq \operatorname{Av}_r(L_{n+1})$ for all $r$.
We need to prove one more fact: $\operatorname{Av}_r(M_{s-1}) < \operatorname{Av}_r(L_s)$ for all $r \geq s-1$.
Edit: As @DavidSpeyer pointed out in a comment, this is easily proved by observing that $M_{s-1}$ is a subword of $L_s$. I've removed my lengthier argument, but left the generating functions $m_n(x)$ and $\ell_n(x)$ defined above.
We now combine all of our results: for $r \geq k$ $$\operatorname{Av}_r(u) \leq \operatorname{Av}_r(M_k) < \operatorname{Av}_r(L_{k+1}) \leq \operatorname{Av}_r(L_m) \leq \operatorname{Av}_r(v).\;\;\square$$