Target practice?

But seriously, there are other parts of the game where shuttle/runabout use is inferred... like boarding parties, or new bridge officer assignments, etc.

And let us not forget the shuttle-type pets.

Shuttle use is also depicted in other missions. You use one to pick up the Vulcan ambassador for the P'Jem mission. I believe there is also a KDF mission where you steal a shuttle to penetrate a Federation facility (haven't played it yet, but I'm looking forward to it).

Really, it's just added Star Trek flavor for the game, and that's a good thing. I'm sure we'll see more shuttle missions in the future now that the shuttle tech has been added.