First, because action $M$ is weakly dominated for Player 3, does everyone assume that $r_2=0$?
Without seeing the game you're considering, it's hard to tell. But the general answer is No. Weakly dominated strategies can be played in a Nash equilibrium (either mixed or pure). In the following game, both $B$ and $C$ are weakly dominated strategies for both players. But each player randomizing between them in any proportion is still a NE.
\begin{array}{|c|c|c|c|}
\hline & A & B&C\\\hline
A&1,1&0,0&0,0\\\hline
B&0,0&0,0&0,0\\\hline
C&0,0&0,0&0,0\\\hline
\end{array}
Does Player 3 need to be indifferent between $L$, $M$, and $R$, or just between $L$ and $R$, since $M$ is weakly dominated?
The indifference condition for MSNE applies to pure strategies in the support of the equilibrium mixed strategy. If $M$ is played with positive probability in equilibrium, then you'd need indifference across all three. If $M$ is played with zero probability, then you'd need $u_3(\sigma_1,\sigma_2,L)=u_3(\sigma_1,\sigma_2,R)\ge u_3(\sigma_1,\sigma_2,M)$
More generally, the necessary and sufficient conditions for a Nash equilibrium (either pure or mixed) are summarized in the following theorem:
A strategy profile $(\sigma_1,\dots,\sigma_n)$ is a Nash equilibrium if and only if for all $i=1,\dots,n$,
\begin{equation}
u_i(s_i,\sigma_{-i})= u_i(s_i',\sigma_{-i}), \qquad \forall s_i,s_i'\in\mathrm{supp}(\sigma_i)
\end{equation}
and
\begin{equation}
u_i(s_i,\sigma_{-i})\ge u_i(s_i',\sigma_{-i}), \qquad \forall s_i\in\mathrm{supp}(\sigma_i)\text{ and }\forall s_i'\notin\mathrm{supp}(\sigma_i).
\end{equation}
Hence, we see that the indifference condition is only required for pure strategies in the support of the equilibrium mixed strategy but not necessarily outside it.