I am thinking of writing a spy thriller, and I am in the process of forming an outline. The plot in my mind involves 3-4 countries and would involve accusing some countries of heinous crimes, as an example say Country A. I have three sub questions:

1. Although fiction, but inspired by real events; countries will have to be named, and can their real names be used? Or should I find fictional names for these countries to prevent unwanted problems?
2. Are there any cases of real life problems due to real names being used? I am sure these won't create any diplomatic tensions, but could these create problems to authors; like prohibit entry of the author to Country A.
3. How are such problems overcome by writers apart from using fictional names? A disclaimer?