A thin record, not an empty one
The Corps did not travel through Shawnee towns on the Missouri. The journals still name the Shawnee twice, and both mentions are worth keeping straight.
On 16 November 1803, after crossing the Mississippi, Meriwether Lewis found Shawnee and Delaware people camped at the upper habitation on the opposite shore:
we found here som[e] Shawnees and Delewars incamped; one of the Shawnees a respectable looking Indian offered me three beverskins for my dog with which he appeared much pleased
That is an Ohio–Mississippi encounter, not a Missouri-river council. Lewis refused the trade. The dog is Seaman.
The second mention is only a comparison. In the long Shoshone ethnography of 19 August 1805 Lewis wrote that Shoshone complexion was “much that of the Siouxs or darker than the Minnetares mandands or Shawnees.” No Shawnee person is on that hillside. The name is a yardstick in Lewis’s head.
A synthesis that claimed the Shawnee were absent from the corpus was describing an empty tag set, not the journals.