A bit of confusion here and I am anot sure which is correc as the Rules feel vague.
when crafting a peperbox (6 barrels) ....
do you pay the masterwork cost (300gp) for the weapon itself or do you pay it for each barrel (300gp x 6)?
when enchanting ... do you enchant the entire thing (like a bow) or do you have to enchant each barrel (like a double weapon)?
It's a single weapon, with no rules to the contrary.
Note that even the double barreled musket is still treated like a single weapon. The only thing that would need to be crafted separately is the warhammer musket, which is of course both a warhammer on its stock, and a musket for the actual shooty part.