Is the 9-speed Sora crankset compatible with 105 11-speed chain? I'm thinking of upgrading my bike, which has a Sora 9-speed system on it (50/34 chainset). The upgrade is for esthetic reasons - i simply like the look of the internal cable routing. That being said, it is not an absolutely essential upgrade, and if it costs too much I will not do it. 

My plan is to buy the new Shimano 105 5800 11-speed cassette, shifters and chain. I understand that the 11-speed chain is thinner than a 9-speed. Does this mean that I also have to buy a new crankset to replace my 50/34 Shimano Compact FC-R345 Octalink?
You should just be able to replace the chainrings for 11 spd ones.

You can also get 9-spd 105 shifters if you just want tidier cable routing (I assume you mean internal as in under the bar tape) which would let you keep the rest of your groupset as is.