For how many more points of damage on arrows is +1PD for you?
I forget what I figured it out to be, as PD is an extra 8 or 14% increase or some such thing like that, so the extra 2 points from masterwork arrows is rather nice. An average archer has a Strongbow and bodkins, so base damage of 25+6=31 damage. With masterwork arrows though this is now 33 damage, a 6.45% increase in damage which coupled with the added ammunition means that your damage output has risen semi-appreciably. Now consider that the Damage Multiplier from WPF (remember, Damage is 0.15*wpf +0.85, small but not totally insignificant) and PD are calculated from the Base damage.
So random number time:Assume that your WPF and PD are, I dunno, giving you an extra 50% increase in damage (conservative for some builds, I know).
ShortBow and Bodkins (31): 46.5
Shortbow and MW Bodkins (33): 49.5
MW ShortBow and MW Bodkins (36): 54So we actually get 3 extra points not two from those arrows from a mere 150% damage multiplier. Consider that some builds will exceed this. With a full MW set, you are talking about an extra 8 damage from a normal set.
I say the damage from arrows is worth it.
EDIT: And someone just smited me in this thread for posting this, so I guess my reasoning is flawed...