Fighters should not count as being ships; that is the theory however, which can be annoyingly quite different from the Truth.
(I will test it out later)
Alarikf, I think I stated in a first post that Non-intercourse treaties had no happiness effect, which was wrong. I think I wrote in a later post that they do give a happiness boost (+10% if you are interested by the numbers, equivalent to colonising ten planets with a peaceful race), but I cannot exactly recall what I posted.
So the clearer explanation is: Non-Intercourse and None treaties (breaking treaties in other words) give happiness boost for neutrals, like having friendly troops and an UPC. Time also puts them back on Indifferent faster than the other happiness types, though it does not work if your people are busy rioting. Everything else does nothing at best, or makes your people unhappy (including winning battles, colonising and capturing enemy planets).