For your first question, the answer is based on your comments.
By Lefschetz (1,1) theorem, $rk(NS(Y))=\dim_\mathbb{Q}H^2(Y,\mathbb{Q})\cap H^{1,1}(Y)$, so for any abelian surface $Y$, we have $rk(NS(Y))\leq h^{1,1}(Y)=4$.
Claim: Suppose $Y=\mathbb{C}/\mathbb{Z}[i]\times \mathbb{C}/\mathbb{Z}[i]$, then $rk(NS(Y))=4$.
Proof: Let $(z,w)$ be the complex coordinate of $\mathbb{C}^2$, the universal cover of $Y$. Here $Y=\mathbb{C}^2/\Lambda$, $\Lambda$ is a free abelian group generated by $(1,0),(i,0),(0,1),(0,i)$.
Consider $\alpha=idz\wedge d\bar z$, $\beta=idw\wedge d\bar w$, $\gamma=i(dz\wedge d\bar w+dw\wedge d\bar z)$, $\delta=dz\wedge d\bar w-dw\wedge d\bar z$, so $\{\alpha,\beta,\gamma,\delta\}$ is a basis for the complex vector space $H^{1,1}(Y)$.
Moreover, it follows by simple calculation that $[\mathbb{C}/\mathbb{Z}[i]\times\{\ast\}]=\beta/2$, $[\{\ast\}\times\mathbb{C}/\mathbb{Z}[i]]=\alpha/2$, $[\{(z,z)\in Y\}]=-\gamma/2$, $[\{(z,iz)\in Y\}]=\delta/2$, so $\alpha,\beta,\gamma,\delta\in H^2(Y,\mathbb{Q})\cap H^{1,1}(Y)$ and they are linearly independent over $\mathbb{Q}$. QED
For your second question, since $K_Y=0$, by Riemann-Roch theorem
$$
h^0(nF)+h^0(-nF)=h^0(nF)+h^2(nF)
\geq \frac{(F^2)}{2}n^2 +\chi(\mathcal{O}_Y).
$$
Therefore, for $n>>1$, either $nF$ or $-nF$ is effective. WLOG, we assume $D=nF$ is effective. Since $Y$ is abelian surface, every curve $C$ in $Y$ is movable (in the sense of algebraic equivalence), so for any two (possibly reducible) curves $C_1$ and $C_2$ we have $(C_1\cdot C_2)\geq 0$. In particular, for any curve $C$ we have $(D\cdot C)\geq 0$.
If $(D\cdot C)=0$ for some curve $C$, together with $(D^2)>0$, the Hodge index theorem implies $(C^2)<0$, we get a contradiction! Thus for any curve $C$, we have $(D\cdot C)>0$, together with $(D^2)>0$, the Nakai-Moishezon criterion tells us that $D=nF$ is ample, so $F$ is ample.
Remark: This argument for your second question applies for any abelian surface $Y$.