You have my sympathies for trying come to grips with this stuff. Fortunately the answer, which is both yes and no, can be explained in the simplest case of a point. A polarization on a pure Hodge structure $H$ of weight $w$ is a pairing $$\langle, \rangle: H\otimes H\to \mathbb{Q}(-w)$$ such that $(2\pi i)^n\langle -, C -\rangle$ is positive definite and symmetric, where $C$ is the Weil operator which acts by $i^{p-q}$ on $H^{pq}$. These conditions known as the Hodge-Riemann bilinear relations imply that $H\cong H^*(-w)$ as Hodge structures, so in this sense $H$ self dual. However, just having such an isomorphism would not give everything else.
If $H$ is replaced by a variation of Hodge structures, then a polarization is flat pairing as above satisfying the Hodge-Riemann conditions on the fibres. For Hodge modules the story is similar but more delicate. Since the whole theory is constructed by induction on dimension of support, a polarization is also defined in this manner. Given Hodge module $H$ of weight $w$ on $X$, a polarization is a pairing $H\otimes H\to \mathbb{Q}(\dim X-w)[2\dim X]$ satisfying the inductive conditions (0.8)-(0.10) of Saito's "Modules Hodge Polarizables". Such a pairing should induce an isomorphism $H\cong DH(?)$ up to twist, but it's not equivalent. (Added I don't have a precise reference or proof for this, just a feeling that one could prove it as follows: Buried in Saito's second paper, "Mixed Hodge modules", is a proof that any simple polarizable Hodge module is $j_{!*}V$, where $V$ is a VHS. This effectively reduces the duality statement to the previous case.)