IIRC there was some thread by peddroelmz about mechanics and usefullness of AP mods/ammo and dmg up barrel mods. Something about that if your rifle etc has over 100 dmg per bullet of something, i don't seem to recall the number, you are better off with barrel mods, but if it's lower, then you'll get more effect on your damage output from armor pierce. Also you can use both to get the maximum result on most guns.
I couldn't find the thread though, I'll keep looking - but I found an interesting one by Cyonan. There it is written that cover piercing shots get dmg reduction from the best of your mods - like if you have mod that shaves off 30% dmg when you pierce cover, and some other mod that shaves 40% - so if you pierce it, you'll have 30% shaved off, because that was the best you could get. But, if you have innate cover piercing, like Javelin or Typhoon, then no damage gets shaved off. Thanks to the innate cover piercing.
EDIT: Found the thread, actually that wasn't peddro's, got fooled by a lot of numbers. Here's it.
Phaeston 47.6dpb [10rps] - Silver = 17.6dpb Gold = 5dpb
AP - Silver = 37.1 Gold = 30.1
EB 59.5dpb - Silver = 29.5 Gold = 9.5dpb
With both - S 49 G 42
Verdict - AP mod wins overall, but EB is not a terrible choice to take on silver runs.