The solution for this would be to search the ships Hardpoint in: scripts/ships/hardpoints
(it's a .py file, you can open it with any standard text editor, like e.g. notepad.
On another Note: Delete the corresponding .pyc file for the changes to have an effect)
and alter the .setRadius values for (both ?) the Shuttlebay and Shuttlebay_OEP (or whatever their actual name is) Properties.
AFAIK no Shuttle (even the horribly oversized ones) is bigger than 0.5 game units.
If that still is not big enough you could get the actual shuttle size in Quickbattle, if you set the Playership to said Shuttle,
open the console ( press ^ (that
could vary depending on keyboard layout))
and type:
import App
import MissionLib
print App.ShipClass_Cast(MissionLib.GetPlayer()).GetRadius()
The Shuttlebay -size must be at least that large.
Oh, also the Console always assumes US / Qwety layout; so if your Keyboard uses something else it would be much less frustrating to search beforehand where stuff like y/z, "_", and the brackets are positioned on that layout.