By extend the Lex do you mean extend the 6? If so, you'd need 2 new tracks BBCH <-> this new terminal to handle the traffic.
I don't think the level of the station underground has much to do with flooding. As soon as you're below the waterline, you're pretty much toast. It's about how the design of the structure copes with that fact that determines how things fare more than everything else. A family member who works for the TA's engineering dept and was doing resiliency stuff post-Sandy mentioned that the new SF filled up "like a bathtub" during the storm. The loops, which had tracks on either side (incl. the Joralemon st tube which lies at a lower level) to empty into, didn't have the same issue, so in that way (water would fill the tubes before the station) a stub terminal would do better, but for all the wrong reasons.