Yes. Copy the Sub Command mission into the DW Scenarios folder. Open the mission in the DW scenario editor, and then save it. The mission will now be a Dangerous Waters scenario.
A couple of caveats:
1) Not all of the Sub Command doctrine options (in the scenario editor) were not carried over to Dangerous Waters. Specifically, some User Actions (e.g., "Raise Radio Antenna") are not in DW. Sub Command scenarios that use any of these items will not work unless you re-edit the scenario to delete/change the problem triggers/goals. :hmm:
2) Sub Command scenarios built for SCX (i.e., with any of the 'new' SCX platforms) will not transfer over to DW unless you re-edit those platforms to some other platform allowed in Dangerous Waters.
Otherwise, I've found the translation between SC and DW to be mostly error-free.
Good luck, and if you redo any of the SC missions for DW, please pass them to me and I'll post them on my site.