Nope, the plan currently is to have no upgrades. When "upgrading", ships will efefctively be scrapped, and the upgrade is built in its place. Some resources from the old design are used for the new design's construction, and it's still on hold what happens to the crew (regarding experience, since Personnel will be ditched in the next version of the game - and be replaced with Leaders).
Real upgrades are not out of the question though. They may be implemented in the future, if Mike finds the time to. Right now, there are more important things.