There isn't any way to manipulate the Decal or Part Type and have a SMT part with a thru-pin show up in the SMT pick-n-place file utilizing the standard outputs provide in CAM Plus. I received the following responses from SupportNet.
"PADS is coded so that any through-hole terminal added to a decal is considered that over surface mount."
"Unless there is something very specific about CAM Plus, the best option for Pick-n-Place file is the #17-Excel VB script output. Or you can
create a custom one using the PADS Layout ScriptWizard. CAM Plus code is rarely updated."
Review this technote: PADS Layout: Options for creating a Part Placement Report for Pick and Place machines