I don't know how to construct (if it exists) an unbiased estimator of the Hellinger distance. It seems possible to construct a consistent estimator. We have some fixed known density $f_0$, and a random sample $X_1,\dots,X_n$ from a density $f>0$. We want to estimate
$$
H(f,f_0) = \sqrt{1 - \int_\mathscr{X} \sqrt{f(x)f_0(x)}\,dx} = \sqrt{1 - \int_\mathscr{X} \sqrt{\frac{f_0(x)}{f(x)}}\;\;f(x)\,dx}
$$
$$
= \sqrt{1 - \mathbb{E}\left[\sqrt{\frac{f_0(X)}{f(X)}}\;\;\right] }\, ,
$$
where $X\sim f$. By the SLLN, we know that
$$
\sqrt{1 - \frac{1}{n} \sum_{i=1}^n \sqrt{\frac{f_0(X_i)}{f(X_i)}}} \quad \rightarrow H(f,f_0) \, ,
$$
almost surely, as $n\to\infty$. Hence, a resonable way to estimate $H(f,f_0)$ would be to take some density estimator $\hat{f_n}$ (such as a traditional kernel density estimator) of $f$, and compute
$$
\hat{H}=\sqrt{1 - \frac{1}{n} \sum_{i=1}^n \sqrt{\frac{f_0(X_i)}{\hat{f_n}(X_i)}}} \, .
$$