Jefferson had delivered in January 1803 a confidential message to Congress that justified the expedition on the grounds of expanding trade with the Indians. Jefferson had also solicited suggestions from scientist and knowledgeable government officials for the types of information that should be sought. He could synthesize the resulting suggestions into a final draft of instructions for the expedition. Jefferson’s instructions concerning Native Americans covered everything from language and law to trade and technology. The explorers were to record Indian foods, what the Indians wore, their technology and handcrafts, and what they believed in. Jefferson told Lewis: “You will therefore endeavor to make yourself acquainted as far as diligent pursuit of your journey shall admit, with the names of the nations and their numbers”. The captains understood that they were to do more than count natives and list languages. From the beginning of the corps of discovery virtually every diarist in it diligently recorded all sorts of information about Indian life.
"Manitou, buffalo, and Indian." Clark's journal, June 7, 1804.
On the whole it is not surprising that Lewis and Clark did not record more information about the Native American rock art that they passed on the way. Given the cultural biases of the time, and their mission from Thomas Jefferson, recording all rock art was just not generally thought worthwhile. We do have to wonder what other things we could have learned about Native American art had attitudes been different.