I'm currently playing a game with everything automated. The focus point is one ship, a small freighter. I'm into the third year now of nothing but observing this one private ship going about its business. It's actually been pretty neat to watch.
I did notice that the ship tried to go in for a retrofit but cancelled it before it got to that point. It may have had to do with a manual upgrade to the small freighter design I tried to insert (the automated design process rejected it by assigning it as not the latest design).
As an aside, it's pretty cool watching the exploits of this one ship and crew. They spent months doing nothing as Caslon was not an available resource initially, but over time colonies sprung up and transport jobs started happening. So far, it's mostly been about moving gases, but there were two jobs that hauled gold and carbon fibre, but those were intrasystem transport jobs.
ORIGINAL: Erik Rutins
The private sector will retrofit ships, but on its own schedule. Older ships may stay in service for quite a while.