I found the solution. There are three ways I've found (so far) to set line numbers. Only one makes them stick. It's buried in the Preferences > Text Status Display > Show line numbers.
For better, or worse, BBEdit can remember display options like soft wrap and line number display on a per-document basis. Documents which have this state stored with them will override the BBEdit setting you found in the preferences.
With only one exception I can think of, settings you want to apply to all new/opened documents should be set from the Preferences window.
What's the exception? Default window sizes are set directly by choosing "Save Default Window" when you have a window in the size and position you like best.
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