Perhaps it is just the shortcuts that are the problem. Have you tried creating new shortcuts for these applications?
You can find the exe's for these applications in the Windows folder:
Excel = pxl.exe
Word = pword.exe
PowerPoint = ppt.exe
See this link for more information about how to create shortcuts on your Pocket PC:
Taking Shortcuts....
If these applications are really missing from the Windows folder, you'll need to perform a clean reset to restore your Pocket PC to factory settings (well post WM5.0 upgrade settings anyway).