How many satisfying assignments are there in a set of 3-CNF clauses where no clause share the same variable? Say I have a set of 3-CNF clauses
$$\mathcal{S} = \{ x_1 \vee x_2 \vee \bar{x_3}, ~~x_4 \vee x_5 \vee x_6\}$$

where $\bar{x}$ is the negation of $x$. Each variable range over $\mathbb{Z}^2$.

How many satisfying assginments are there for $S$? In general, how many satisfying assignments are there for $S$ is the size of $S$ is k?

This is a question about what is a satisfying assignment for 3-disjunctive clause as much as it is about counting. For example when I just have $C = x_1 \vee x_2 \vee \bar{x_3}$, there are $2^3 = 8$ possible assignments:
$$1 1 1\\
0 1 1 \\
1 0 1\\
1 1 0\\
1 0 0\\
0 1 0\\
0 0 1\\
0 0 0
$$
But which one of these are satisfying assignments?
As you noted, for every clause there are $2^3$ possible assignments. Exactly one of them does not satisfy the clause: it's the one that has false for all variables that appear in the clause as a positive, and true for the variables that appear as a negative. In your example it is $001$. The rest of the assignments satisfy the clause. Therefore there are $2^3 - 1 = 7$ satisfying assignments for each clause, which means there are $7^k$ possible assignments in total.