Is a composition of clocked entities a clocked entity in the UC model?
When you compose $2$ interactive systems $\mathcal{IS}_1$ and $\mathcal{IS}_2$ into $\mathcal{IS}_1 \circ \mathcal{IS}_2$, the book indicates that you're simply connecting the matching ports between them.

In your example $\mathcal{IS} \circ D$ is a clocked entity because when $B$ calls $D$ then $D$ makes a recursive call to $\mathcal{IS}$ by sending the token to $C$. Taking from the book: "When it is clocked it must eventually
return the activation on the matching outport leak" not immediately.

Regarding your second question:

You can think of a synchronous execution as a single thread program execution which goes from one line to the next one. Each line represents an agent and the clock can be here the line number. The clock is just a flag to capture which agent is running at a given time.