I read a few days ago that, irregardless of how you design the freighter, once the route starts game mechanics take over, and you have a freighter moving at speed 1 along the route. Personally, I think this is a poor design decision; if you have tech to design a fast freighter, and are willing to pay to maintain it, why can't the freighter move at the s25 or whatever you designed?
That aside however, I'm wondering about this as it might relate to arming freighters. If I design a freighter that includes weapons and defenses, are these going to be used if an enemy jumps the freighter while it's bumbling along at s1, or are they also removed when the trade route mechanics take over?