You can make objects when you are initially modeling them any size you want really as it's just a question of scaling them down to the proper size. For a reference you might check out the sample XSI content that comes with the SDK, I'm pretty sure all the weapons are stored in there.
model the weapon in "real scale" so that it is the real size it would be in real life. eg a pen which is 4 inches. then put the scale factor to 39 in your qc and that will chang it to "real scale" in hl2.
