Thank you, Michael, for answering my previous question. It seems that I overlooked the problems in my initial question. I didn't recognize the SDP (in either primal or dual form) even for the 2-norm constrained problem. Now, I have a better understanding, I have another question.
For exact low rank matrix completion the corresponding SDP is:
$\text{minimize}_Y~\text{trace}(Y)$ subject to $\langle\left[ \begin{array}{cc} 0 & P_{ij} \\ P_{ij}^T & 0 \end{array} \right], Y \rangle = 2M_{ij}, \forall (i,j)\in\Omega$ and $Y \succeq 0$
where $P_{ij} = e_ie_j^T \in \mathbb{R}^{m \times n}$ and $Y$ is the matrix $\left[ \begin{array}{cc} W_1 & X \\ X^T & W_2 \end{array} \right]$ in the original question. This problem has $|\Omega|$ equality constraints.
Now, we consider the noisy matrix completion problem with 2-norm constraint. I think, one SDP formulation is as follows: Let $w$ and $x$ are the vectorized versions of $(W_1,W_2)$ and $X$ and $c$ is the appropriate binary mask vector to get the diagonal entries of $W_1$ and $W_2$.
$\text{minimize}_{w,x}~~c^T\left[\begin{array}{c} w \\ x \end{array} \right]$ subject to
$\displaystyle\sum_{ij\in\Omega}x_{ij} F_{ij} + \displaystyle\sum_{ij\notin\Omega}x_{ij} G_{ij} + \sum_{\begin{array}{c} i\le j \\ ~1\le i,j \le m \end{array}}w^{(1)}_{ij}H_{ij} + \sum_{\begin{array}{c} i\le j \\ ~1\le i,j \le n \end{array}}w^{(2)}_{ij}K_{ij} - E \succeq 0$
where
$F_{ij} = \left[ \begin{array}{c|c} \begin{array}{cc} 0 & P_{ij} \\ P_{ij}^T & 0 \end{array} & 0 \\ \hline 0 & \begin{array}{cc} 0 & P_{ij} \\ P_{ij}^T & 0 \end{array}\\ \end{array} \right]$,
$G_{ij} = \left[ \begin{array}{c|c} 0 & 0 \\ \hline 0 & \begin{array}{cc} 0 & P_{ij} \\ P_{ij}^T & 0 \end{array}\\ \end{array} \right]$;
$H_{ij} = \left[ \begin{array}{cc} Q_{ij}+Q_{ji} & 0 \\ 0 & 0 \end{array} \right]$, $Q_{ij}$ is a $m \times m$ matrix with 1 at $(i,j)$ and 0 everywhere else;
$K_{ij}$ is defined similarly to $H_{ij}$
and $E = \left[ \begin{array}{c|c} \begin{array}{cc} -\epsilon I & \mathcal{P}_\Omega(M) \\ \mathcal{P}_\Omega(M)^T & -\epsilon I \end{array} & 0 \\ \hline 0 & 0 \end{array} \right]$.
The Frobenius-norm constrained problem can be formulated similarly by stacking.
My formulation above (if correct) seems to be quite naive and taking its dual form results in many equality constraints (~$(m+n)^2$).
While having more constraints/variables seems to be unavoidable for noisy problems, I am wondering if there is any better formulation with fewer equality constraints.
Thanks.