The reason Thomas Jefferson gave American explorer Meriwether Lewis a cipher was that his expedition was not only scientific and commercial but colonial. Jefferson knew that all those vast lands and territories were to be taken by the United States to keep Spain or Britain from taking them first. He understood that having an access to the Pacific Ocean would provide a great position for the new nation to commerce with Asia. Thus, he made sure to provide Lewis with a way to communicate with him secretly in the event that both him and William Clark were ever captured by military forces of the rivaling European powers or even by the Native Americans.
Indeed, the Spanish Empire had claims to the lands that Lewis and Clark were exploring and the existence of the expedition was disclosed to them by American general James Wilkinson, who was a paid spy for the Spaniards. Four armed Spanish expeditions were sent by the Spanish Authorities to capture and interrogate Lewis and Clark but they were never able to find them.
