It is possible to modify a ship class, even when some ship of that class are already built, even when SM mode is turned off (I turned it on and then off because I heard a rumor there was a related bug). When doing so, the already built ships also get modified.
I discovered it this way:
Make 2 cargo ships to get infostructure to Luna
Forget to add Shuttles Cargo Bays
Luna doesn't have a Space Port.
Realize I need Shuttles Cargo Bays
Add said Shuttles Cargo Bays to my Cargo Ship class.
My two cargo ships, which were already on their way to Luna, now have Shuttles Cargo Bays.