Note that this is equivalent to asking whether any finite index subgroup of $H$ is dense. In particular there's no real reason to consider the situation within an ambient algebraic group $G$.
If you assume irreducibility, or even connectedness, of $H$, the claim is true as the only finite index closed subgroup of $H$ is $H$ itself (This follows as $H$ is the union of the cosets of any such subgroup), yet the closure of any finite index subgroup will be a finite index subgroup as well.
Without assuming connectedness of $H$ the claim is not true. Consider for example $H_0\subsetneq H\subsetneq G$ finite groups.