As for why, run the mission Weapons Free once. Tally up your loot (remembering that the limit probably kicked in about half way through). Multiply by how many times you can run that in short order. If that's less than entirely too much, run it again with heavy use of torpedo spread and redo the math.
It doesn't apply to anything else, and I've hit it plenty of times and still gone on to get all kinds of loot from non-Foundry content.