I don't think the problem has anything to do with vis-only roads. I did a create all on my test terrain and with no vis-only roads there were still no trains etc running. Then I deleted all roads, added a single road supplying an airfield and built the terrain again, still no trucks running after 10 mins. Finally I converted this road to a river, but still no barges. I think something has changed in one of the game updates released between when I first tested the road system and saw barges offline and now.