It seems, with the following lemma, the proposition at the bottom easily follows.
If $Y\subset X$ dense. Then, for every nonempty $A\subset Y$, $\text{Int}_Y \left(\text{cl}_Y A\right)=Y\cap \text{Int}_X \left(\text{cl}_X A\right)$.
Proof. Since $Y$ is dense in $X$, we have $$\text{cl}_X \left(\text{cl}_Y A\right)=\text{cl}_X A; \quad \text{cl}_Y A=Y\cap \text{cl}_XA;\quad Y-\text{cl}_Y A=Y\cap \left(X-\text{cl}_XA\right).$$
If $\text{cl}_Y A=Y$, using the first equality, the conclusion can be easily verified. Suppose $\text{cl}_Y A\subsetneq Y$. Then, the third equality implies $Y-\text{cl}_YA$ is dense in $\text{cl}_X\left(X-\text{cl}_XA\right)$. Combining this with the second equality, then $\text{cl}_Y \left(Y-\text{cl}_YA\right)=Y\cap \text{cl}_X\left(Y-\text{cl}_YA\right)=Y\cap \text{cl}_X\left(X-\text{cl}_XA\right),$ and so \begin{align*} \partial_Y \left(\text{cl}_YA\right)&=\text{cl}_YA\cap \text{cl}_Y \left(Y-\text{cl}_YA\right)\\ &=\text{cl}_YA\cap Y\cap\text{cl}_X \left(X-\text{cl}_XA\right)\\ &=Y\cap \text{cl}_XA\cap\text{cl}_X \left(X-\text{cl}_XA\right)\\ &=Y\cap\partial_X \left( \text{cl}_XA\right). \end{align*} Therefore, $$\begin{align*} \text{Int}_Y\left(\text{cl}_Y A\right) &=\text{cl}_Y A- \partial_Y \left(\text{cl}_YA\right)\\ &=Y\cap \text{cl}_XA- Y\cap\partial_X \left( \text{cl}_XA\right)\\ &=Y\cap \left(\text{cl}_XA-\partial_X \left(\text{cl}_XA\right)\right)\\ &=Y\cap\text{Int}_X \left(\text{cl}_X A\right). \end{align*}$$ $\square$
Proposition. If $Y\subset X$ dense. A subset $A\subset Y\subset X$ is nowhere dense in $X$ iff it is nowhere dense in $Y$, where $Y$ is given its subspace topology.
Proof. If $A$ is nowhere dense in $Y$, by the lemma, $Y\cap \text{Int}_X \left(\text{cl}_X A\right)=\text{Int}_Y \left(\text{cl}_Y A\right)=\emptyset$. But since $Y$ is dense in $X$, $Y\cap \text{Int}_X \left(\text{cl}_X A\right)=\emptyset$ iff $\text{Int}_X \left(\text{cl}_X A\right)=\emptyset$. Hence $A$ is also nowhere dense in $X$. The other direction is even easier, given the lemma. $\square$
Are there any mistakes? Thanks in advance. (Motivated when answering this question.)
Update:
After searching through the internet for a few days, I found the following proposition in a book called Baire Spaces, by Haworth and McCoy (1977). But it only says "a similar proof" can be given to when $Y$ is dense in $X$, without actually providing it. 
All correct, as far as I can see.
I find the following easier to understand, but that's just personal opinion.
For any $Y$, dense or not, $(cl_X A) \cap Y = cl_Y A$. Hence $int_X(cl_X A) \cap Y \subseteq cl_Y A$ and so $int_X (cl_X A) \cap Y \subseteq int_Y(cl_Y A)$.
The other direction does use denseness. Let $U$ be any open set of $X$ such that $U \cap Y = int_Y(cl_Y A)$. As $cl_Y A \subseteq cl_X A$ we have $(X \setminus cl_X A) \cap (U \cap Y) = \emptyset$. By denseness $(X \setminus cl_X A) \cap U = \emptyset$, and so $U \subseteq cl_X A$ and $U \subseteq int_X(cl_X A)$. Therefore $int_Y(cl_Y A) \subseteq int_X(cl_X A) \cap Y$.