This is a stupid kludge, but it works.
Copy your list, with checked/unchecked boxes.
Paste into a Word document (no, notepad does not work -- it will include brackets and Xs)
Copy the list from Word back to Evernote. Now you have a plain text list without checkboxes.
Select the list in Evernote, hit Shift-Ctrl-C. (Or the comparable combination on a Mac)
Now you have a clean list with unchecked boxes.