I tried the steps from "Vector Tools Missing in QGIS 1.8 Ubuntu""Vector Tools Missing in QGIS 1.8 Ubuntu". Most of the tools under "Vector" are missing from my recent installation of QGIS 2.18.2, so I am unable to clip, buffer, make Voronoi polygons, etc. Python appears to be running correctly and I have checked to ensure my plugins are updated and enabled. For some reason "ftools" plugin is not availabe when I search for it in Plugin Manager under "All".
EDIT: I did a clean reinstall of QGIS and this fixed the problem. I think there was an old version of GDAL causing the problem.