It's not possible, you need Gerbtool to do that function which is no longer bundled with EWB suite. Most of the times the PCB manufacturer will do this for you. If you try to block copy and paste, it automatically updates the refdes values incrementally......It has been discussed before...right now, Gerbtool is the only solution.
What about doing it as a multi-page design in Multisim and using the Refdes offset feature in the renumbering tool? Obviously you don't get a 3D view of the PCBA, but you can still keep the boards sorted as in R101, R102, R103 on board 1 and R201, R202, R202 on board 2.
Yes, any silk over a copper pad or contact for soldering point, by IPC standards, is a DRC violation. Even though NI doesn't flag for it (which is SHOULD), as the numbers get larger (2 and 3 digit), you risk this error showing up and if you were doing production and/or pick and place population could get quality issues in the soldering of the joint as the silkscreen material is mixed into the joint.....a failure waiting to happen.
But that's all assuming a very dense board population. I thought you were referring to DRC flags being raised by having silkscreen over traces and other masked copper, which is crazy. I know from experience in production that 3-digit refdes numbers do not necessarily have to crowd the board, even with pick-n-place assembly lines. Until you have a problem, there is no problem.