To me it looks like not a single wad file is wad included, with the exception of zhlt.wad.
If you look at your hlcsg.exe parameters:
hlcsg.exe mil_duty10 -cliptype precise -estimate -chart -wadinclude d:\wads
...you'll see that the -wadinclude option targets a directory, rather than an actual wad file. You'll need to call -wadinclude for every wad file you want to include in your bsp, so the list of parameters for hlcsg.exe can get quite long, depending on the number of wad you want to include.
Also, have you loaded more than 8 wads in Hammer? Having more than 8 wads loaded could cause problems with compiling, not sure about that though. It was a thing way back in the early days of mapping. I always load no more than 8 wads in Hammer.
As for the map name itself, it doesn't matter where it's placed in the commandline parameters. I'm using my own Compilator for compiling, and it places the map file name at the beginning of the commandline, before all the switch options. It has never been a problem.