Will a person be held accountable for the atheistic whispers that come to his mind, and will he be considered a disbeliever because of them?

I congratulate you on your observance of prayers and seeking refuge in Allah from whisperings (waswas). There is no blame upon you for what happened, and you are neither an atheist nor a disbeliever. However, it is incumbent upon you to desist from these whisperings and not to dwell on them. Rather, turn away from them and seek refuge in Allah the Almighty. For the Messenger of Allah, peace and blessings be upon him, said: "People will keep on asking questions until it is said: 'Allah created the creation, so who created Allah?' So whoever experiences anything of that, let him say: 'I believe in Allah.'" In another narration: "Let him seek refuge in Allah and desist." It has come in the hadith that what a person finds within himself of whisperings which he deems too great to utter is "pure faith." And the Prophet, peace and blessings be upon him, praised Allah who reduced the stratagem of Satan to mere whisperings.