I tried the steps from "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.