Yes, you can delete old projects after importing into CCS v5. Also, you'll need to update the compiler for each project to the latest version.
Bring up the properties by right-click on the project. Select "Properties". In the window, click "General" in the left column. On the right side, there is a dropdown for "Compiler Version". Change it to TI v4.0.0.
Although changing the version is not completely necessary, it will eliminate notices about using the old compiler and it is much faster.