$\{0,1/3,2/3,1\}$ logic has the following connectives:
$\neg r= 1-r$
$r\wedge s=min\{r,s\}$
$r\vee s=max\{r,s\}$
$r\rightarrow s=min\{1,1+s-r\}$
$r\oplus s=min\{r+s,2-r-s\}$
$r\leftrightarrow s=min\{1+r-s,1+s-r\}$
Assume there are countably many atoms. All connectives are allowed in constructing the set. But truth constants are not allowed.
I know that sets like $\{A_{k+1}\rightarrow A_k: k \in \mathbb{N}\}$ or $\{A_i \vee A_j: i,j\in \mathbb{N}, i\neq j\}$ have $\aleph_0$ truth assignments satisfying them in $\{0,1\}$ logic, but I cannot think of an example that furthermore has $2^{\aleph_0}$ truth assignments satisfying it in $\{0,1/3,2/3,1\}$ logic. Any hints?
I assume throughout that "satisfies" means "gives truth value $1$" in your four-valued logic.
Given an atom $A_i$, consider the sentence $$(*)_i:\quad (A_i\vee\neg A_i)\rightarrow A_i.$$ The truth assignments satisfying $(*)_i$ in two-valued logic are exactly those giving $A_i$ truth value $1$, while the truth assignments satisfying $(*)_i$ in your four-valued logic are more complicated. There are two key points:
Truth assignments giving $A_i$ value $0$ or $1$ give $(A_i\vee \neg A_i)$ value $1$, while truth assignments giving $A_i$ value $1\over 3$ or ${2\over 3}$ give $(A_i\vee \neg A_i)$ value $2\over 3$.
A truth assignment satisfies an implication $X\rightarrow Y$ iff it gives $Y$ a truth value at least as large as the truth value it gives $X$.
Putting these together, we get a characterization of those truth assignments satisfying $(*)_i$:
This gives rise to a theory which behaves very differently in the two logics in consideration, namely $$\Theta=\{(*)_i: i\in\mathbb{N}\}.$$ There are continuum-many truth assignments satisfying $\Theta$ in your four-valued logic, but only one truth assignment satisfying it in two-valued logic.
Of course this doesn't answer your question yet since $1\not=\aleph_0$, but it does give an important first step. In particular, by combining $\Theta$ with a theory which has $\aleph_0$-many satisfying truth assignments in each logic you'll get what you want: