For build costs and bombing damage modifiers, negative is good; for other modifiers positive is good. A modifier can either be in % or absolute value.
It seems to me that ship build cost modifier is very powerful. While other modifiers only affect one planet, ship build cost modifier can have an empire wide impact. In the extreme situation, when you are building all your ships on a planet with "Efficient Ship Factories" (-30% ship build cost) and not spending money elsewhere, the bonus is effectively increasing your post-upkeep empire-wide income (credit+metal+crystal) by 1 / 0.7 = 42.8%.
