I do not understand why the dense set would help you in this situation as nonempty sets can still have zero Hausdorff measure. In this answer I will denote the $2$-dimensional Hausdorff measure by $\mathcal{H}^2$ (using the absolute value seems very misleading to me). In the comments I gave some heuristics. Let me back this up by something a bit more rigorous.
As I pointed out in the comments it depends on the desired notion of boundary (either withing the manifold with the subspace topology or in $\mathbb{R}^3$). As you are using $\{ f> 0 \}^c = \{ f=0 \}$, you seem to take the boundary within the manifold. In this case, your claim is not true. Consider
$$\mathbb{T}^2 = \{ (x,y,z) \in \mathbb{R}^3 \ : \ (x^2+y^2-2)^2+z^2 =1 \}$$
(some 2-dimensional torus) embedded in $\mathbb{R}^3$. This is a compact, smooth manifold. Now consider the map $f: \mathbb{T}^2 \rightarrow \mathbb{R}, f(x,y,z)=z^2$. Then $f$ is a smooth, nonnegative map. However, the boundary of the zero locus is equal to two circles (1-dimensional manifolds) and thus, the $2$-dimensional Hausdorff measure will vanish.
If you were to pick the boundary in the topology of $\mathbb{R}^3$, (meaning, the balls should intersect $\{ f>0 \}$ and $\{ f>0 \}^c$), then you get $\{f>0 \} \subseteq \partial \{ f>0 \}$ (that is because any ball in $\mathbb{R}^3$ intersects $M^c$). However, $\{ f>0 \}$ is an open subset of a $2$-dimensional, $C^{1,\alpha}$ manifold and thus is a $2$-dimensional $C^{1,\alpha}$ manifold itself. However, nonempty $2$-dimensional $C^{1,\alpha}$ manifolds have positive $2$-dimensional Hausdorff measure. As $M$ is embedded, for every point $p\in M$ there exists a diffeomorphism $\varphi: B_1(0) \rightarrow \mathbb{R}^3$ such that $$\varphi((-1,1)^3) \cap \{ f>0\} = \{ \varphi(x,y,0) \ : \ (x,y,0)\in (-1,1)^3 \}$$
and such that $\varphi(0)=p$. By the monotonicity of measures, we get
$$ \mathcal{H}^2( \varphi([-0.5, 0.5] \times [-0.5,0.5] \times \{0\})) \vert \leq \mathcal{H}^2( \{ f>0 \} ) \leq \mathcal{H}^2( \partial \{ f>0 \} ). $$
However, as $\varphi$ is $C^1$, we have that its restriction to $[-0.5,0.5]^3$ is bilipschitz (lets say with the inverse having lipschitz constant equal to $L$). By Measure of image of Lipschitz function is bounded? (the $C^{1,\alpha}$ regularity actually would allow you for a simpler proof of this fact, in fact we do not really need $M$ to be more than a topological manifold, see the next paragraph) we have
$$ 0<1 = \mathcal{H}^2([-0.5,0.5] \times [-0.5,0.5]\times \{0\})=\mathcal{H}^2(\varphi^{-1} \varphi([-0.5, 0.5] \times [-0.5,0.5] \times \{0\}))
\leq L^2 \mathcal{H}^2(\varphi([-0.5, 0.5] \times [-0.5,0.5] \times \{0\})). $$
Hence, we get
$$ 0< 1/L^2 \leq \mathcal{H}^2(\partial \{ f>0\}). $$
Added: The $C^{1, \alpha}$ assumption is not really need. Everything works in the topological setting if your manifold is locally given as a graph. Then we can use the projection map. I.e. we have
$$ \mathcal{H}^2((-1,1)^2)=\mathcal{H}^2(P(\{ (x,y, g(x,y)) \in \mathbb{R}^3 \ : \ (x,y)\in (-1,1)^2 \})) \leq \mathcal{H}^2(\{ (x,y, g(x,y)) \in \mathbb{R}^3 \ : \ (x,y)\in (-1,1)^2 \}) $$
where $g$ is any map (we need no regularity, only the fact that we can write it as a graph) and $P: \mathbb{R}^3\rightarrow \mathbb{R}^2, (x,y,z)=(x,y)$ is the projection. So you only need the estimate for the projection which is much easier to show (also because it has all the regularity one can hope for).