I'm not sure if this is possible given the looseness of KML files, but I have a couple thousand KML files that I would like to convert to SHP files. They are almost exclusively line or point data. I believe it is mostly possible to convert kmls via a GUI functionality in QGIS or ArcGIS but I would hopefully be able to do them all at once via command line.
Well there is two options to do this that I can think of. One would be to write a very simple loop within model builder or Arcpy with Arcgis and use the KML to layer tool. Without the KML files I don't know what your results would look like. The other more comand line based option would be using GDAL. Your question is almost idential to How to convert between KML and Esri's shapefile (SHP) format? I would recommend checking that out as this is probably a duplicate.