The article states that some Korean tourists think that the characters, especially the green one, might be caricatures of the country's president Lee Myung-bak. Tensions between the two countries have been running high over territorial disputes, among other issues.
The article did point out that, well, the Kobito Dukan characters debuted in 2006, pre-dating when the current Korean President took office in 2008. However, the article then stated there's also a fat and bald character in Kobito Dukan that looks like former Korean President Chun Doo-hwan. He was president from 1980 to 1988. And I guess he has the monopoly on bald guys with glasses? And maybe the artist who created Kobito Dukan knew that there would be political tensions between the countries in the future? Dun dun dun.
In Japan, Kobito Dukan are "kimo-kawaii" characters, meaning that they are both creepy, yet cute. They certainly don't seem to have a political agenda whatsoever, and their raison d'être is aesthetic. The only statement they seem to be making is a stylistic one, standing apart from the stereotypically kawaii characters in Japan. It's rather surprising that someone in the Korean mass media would draw parallels between these creepy-cute characters and their own political leaders.