No, use the original .png files, you CAN open them with VTFEdit, iirc you need to do Import not Open. They do appear in a weird background color, but don't worry they are transparent once converted to .vtf and once in game.
The vmt i used looks like that (as original gmod icons):
"UnlitGeneric"
{
"$basetexture" "silents_server/scoreboard/icon_pack_1/icon_01"
"$ignorez" 1
"$vertexcolor" 1
"$vertexalpha" 1
"$nolod" 1
}