I'm honestly not trying to be rude, but I doubt (like 99%) that ANY scanning was done whatsoever in the creation of this game. Maybe concept art on paper. Many artists just sketch out in Flash directly.
There is no way to know for sure, but I'm pretty sure the assets (graphics) were either created as all raster (pixel) or started as vector and then were ported into a program like Photoshop or GIMP to be finished as raster.
There are a few ways to go about creating assets like those featured in the game. When I create graphics like these, using Photoshop, everything starts as a single color shape. Using selection tools I isolate areas of the shape, (like the cockpit of the ship, thrusters, and gun pods for example.) copy those areas, and paste them into their own layers. Then I use effects like color-overlay, stroke, bevel/emboss, and others; flattening them into their respective layers as needed. (So effects can be laid over each other.)
Alternately, I will draw an unshaded ship in Flash by hand instead of starting with a flat shape (outlines and color) and then finish it in the method described above.
Tentative title image for the game I'm currently creating with Construct2coffeennicotine2012-08-15 05:37:50