Maybe FS fighters have vectorable thrust like the Harrier or something that allows them to handle like VTOLs, eliminating the need for a landing gear. Since bombers are "sitting" on the floor, and their shape allows them to do so, they probably use a similar method.
Now, let's get to fighters with ventral fins like the Herc II. The most obvious way of landing would be landing like a VTOL retracting that long fin. However, that fin does not look like it's retractable. The other way would be to hover without landing, and let the fighter be "captured" by a crane, that puts it on its platform.
Or you could use the same method used to land F9C Sparrowhawk fighters on the US Navy airships USS Akron and USS Macon: you mount an hook on the top of the fighter, and you must catch a trapeze with that (if you played Crimson Skies, you know what I mean).