Second countable space $X$ has a countable base
$$\mathcal{B} = \{U_i\}_{i=1}^{\infty}$$
Since every open set $U$ is of the form
$$U = \bigcup\mathcal{B}^{'}\mbox{ where } \mathcal{B}^{'}\subseteq\mathcal{B}$$
then it is clear that $X$ has at most $2^{\aleph_0}$ open sets and thus at most $2^{\aleph_0}$ closed sets.
Let's consider three cases:
1) $X$ is $T_1$. Then every point is a closed set. In particular there are at most $2^{\aleph_0}$ points and since Borel $\sigma$-algebra is a subset of a power set, then the size of Borel $\sigma$-algebra is at most $2^{2^{\aleph_0}}$.
2) $X/\sim$ is $T_1$ where
$$x\sim y\ \mbox{ if and only if }\ \bar{x}=\bar{y}$$
where on the right side we have closures. Consider a map
$$F:\mathcal{P}(Y)\to\mathcal{P}(X)$$
$$F(A) = \bigcup_{a\in A}a$$
Note that $A$ is a set of equivalence classes which are sets themselves and thus the definition makes sense. This function is "1-1" between closed sets and it obviously preserves countable unions and intersections. Thus it is "1-1" between Borel $\sigma$-algebras so it follows from 1) $X$ has at most $2^{2^{\aleph_0}}$ Borel sets.
3) $X$ does not satisfy 2). TODO.