All of these questions should be directed to the author directly rather then people who have never work on his/her project. I do recommend emailing the author with these questions.
1. They could be rendered models, hand-draw, drawn in an art package, photographs, potentially anything and then put together with an art package.
2. They are designed and then the logic is put together in script or code. As for web resources, no not really as the question is too vague. Puzzles are just game logic and game design.
3. In a 3D art package like Maya, 3DS max, Cinema 4D, Lightwave, Blender, Milkshape etc. They are 'triggered' again by game logic code or script.