Many leagues around the world publish contract information so the game is 100% accurate for these leagues, e.g. MLS and A League. As for England, they can access clubs' annual financial reports to create estimates. They talk to current players and ex-players and find out what they were earning to refine their estimate. Also many of their researchers have contacts with the clubs they are researching.
Basically, they go to exhaustive and in some cases extreme lengths to gather data on players. Although they can't be entirely accurate for each individual, the overall wage spend is accurate and their margin for error is a small one. The idea that it's 'just a computer game' betrays ignorance of what is the most detailed database of footballers in the world. There is no better-researched resource in football. I said I think their financial figures are 'pretty accurate' and I stand by that.