"-nowadtextures" and "-wadinclude" are two different ways to include the textures inside the bsp.
"-nowadtextures" includes all used textures inside the bsp. This can be both a good and bad thing, lets say your map mostly uses textures from the default halflife.wad then those textures will be included in the bsp even though everyone already got those textures making the bsp unnecessary big. But if you're using mostly custom textures then nowadtextures is a quick 'n easy way to include the textures inside the bsp.
"-wadinclude" includes only the wads you specify to the bsp, eg:
hlcsg -wadinclude mywad1 -wadinclude mywad2 -wadinclude mywad3
So you only wadinclude the custom wads you are using and only those will be added to the bsp.