I don't think there will be any major technological advances that make factory-made guitars significantly cheaper and better than they are now. I think a more interesting direction is for guitars to become simpler and easier to build to the point where a non-expert can build one easily without a lot of exotic tools. (In a way, this has always been the case. Cigar box guitars are an old tradition; they're ridiculously easy to make, and can sound very good.)
If you think about it, a Fender Stratocaster is a very minimalistic design that was engineered to be easy to manufacture with 1950's woodshop tools (bandsaws, routers and jigs, etc).. Every Strat clone is a reproduction of a design made for that era of technology. When CNC machines came on the scene, a Strat shape isn't substantially easier to make than any other shape, but we keep using that shape because it works well and because of tradition.
A guitar design that's optimized to be easy for a non-professional to make with a CNC router and a laser cutter and some basic woodworking tools might look somewhat different. This could open the door to extreme customization -- one-of-a-kind harp guitars, unusual pickup arrangements, guitars with three strings and four frets, nine string guitars designed for 31-tone equal temperament or just tunings, or whatever you like.
I expect most guitar buyers will continue to buy traditional Fenders and Gibsons and so on with 6 strings and from 21 to 24 frets and a scale length of 25 inches, plus or minus half an inch. However, for those that want something different, there will always be a minority of tinkerers who build their guitar just the way they like it. That's where I think the most interesting advances are going to happen.