They are independent players, meaning that they are not directly under the control of the Korean National Badminton Federation.
Similar case with Goh Liu Ying and Chan Peng Soon from Malaysia, who are Malaysia's best pair in the Mixed Doubles discipline but didn't play in the Sudirman Cup due to being independent players...
But I agree, having Ko/Shin and any combination of Lee Yong Dae, Kim Gi Jung and Yoo Yeon Seong would have improved their chances by quite a bit for the Thomas Cup.
(Btw, Yoo Yeon Seong and Kim Gi Jung recently won the Korean National Championships against LYD and Choi Sol Gyu in the final. Would love to see Yoo back on the international circuit, he still has the skills to play at a high level in this currently rather weak MD era)