"In service" is defining "ships." It means ships that are currently being used. The opposite would be "ships that are no longer in service" (they're no longer used) or "ships that are not currently in service" (they're not being used right now- perhaps they're being repaired.)
"In service" isn't normally used with a noun like "guidelines." It's usually used with mechanical things that wear out over time like ships, boats, planes, cars, trucks, and major appliances.
One slightly different use is with taxis. If a taxi is "in service", the driver either has passengers or is looking for passengers. The opposite is "off duty."