Boarding Shuttle disappears?

Yes, with one boarding hangar you can only have 1 captured ship. If you want more you have to build more boarding hangars (If I remember correctly, my old mind might be failing me here )

This might be a reply to an old/discontinued/updated issue, but as far as I have played you can only capture and hold one ship at a time. The shuttle bay becomes obsolete after you take an enemy vessel, unless you plan on sacrificing your current bounty by enemy fire and replacing it with a new captured vessel, for example upgrading your captured ship to a higher level enemy ship.