While I don't think the Photoshop 3D tools are right for everything - they make easy work of extruding graphics, and might make nice cookie cutters. There are a few tutorials out there - you could probably develop a pretty good workflow for scanning sharpie drawings and extruding them to 3D, especially if you happen to be comfortable with graphics programs already.
You may be better going the CAD route ultimately. There's no "make a cookie cutter" program. But you can design cookie cutters in nearly any CAD program out there.
I haven't done much with Autocad Fusion 360 - but it's a pretty well developed program. And with an affordable monthly subscription, it's not a bad choice for a budding business.