Is it possible that the type 10 shuttle is not listed in the shipyard? I got the DS9 bundle and eventually discarded my type 10 shuttle, because I did not like the design.
But it would be great if you could reacquire the things you once bought. For example I got the Delta Flyer then threw it away after some time to make room for a new ship (I initially did not want to buy two additionally ship slots). Again after some time I retrieved the Delta Flyer back from the shipyard for free. But I could not find the type 10 shuttle in the shipyard list.
For the sake of completeness, Cryptic should list the type 10 shuttle in the shipyard.