There is a picture of an auxillary craft in the underside of the D'kora. It the equivalent of the Calypso or Captain's Shuttle. This would be a nice add for C-Store (and a discount issue for those with a D'kora Marauder).
Yes, the Ferengi Shuttle was in the Ferengi lockbox version of the C-store. I believe it indeed cost a hefty 800 points, and that's why you don't see many of them.
To be honest I DO tend to agree that the KDF needs more small craft options, and honestly more ships in general. Of course that's not really a priority because right now there aren't that many small craft missions. If they ever expand content that might be an issue, but right now it pretty much just applies to The Vault, and a couple of missions like one section of the 2400 line.