The actual weapon issue came from the wings. They were far too big. They were designed for a massive cross-range, such as a single surprise overflight then return to the launch center rather than risk overflying the target twice. That looked very much like a weapons delivery profile.

The cargo retrieval potential was also suspect. Nukes are the one thing that could never be de-orbited into the atmosphere. Shuttle looked like something that could enable nuke weaponry in orbit.