The way it worked for splinter cell (afaik) is that Clancy had pretty much little to do with the story and the characters. All Clancy did was approve the technology and politics of the game, to make sure that they were close to realism.
From my understanding, the "Tom Clancy's" brand that is slapped on so many things are just a way of attracting people to a particular product that is starting out. To be quite honest, I probably never would have played splinter cell in the first place if it didnt have the Tom Clancy brand on it, but then again, I'm a huge Clancy fan, and hence the point of putting the brand on it.
I remember hearing about the splinter cell dev team getting into a argument with Clancy over the possibility of the Night Vision/Thermal Goggle hybrid, with Clancy saying it is not possible, but the dev team were able to sway him.
Long story short, I don't think he actually owns the IP, its just a brand name that is put on as a form of advertising (a way of saying "if you like Tom Clancy stories, you'll love this, too"), and is paid royalties for the use of the name.