How can I prevent Notion items without a project from syncing to Todoist?

You can create a formula property in Notion called "Should sync" with the formula if(empty(Project), false, true) . This will identify items with a project assigned.

Then, in your automation, refresh the Notion fields in the filter settings and then add a filter to include only items where Should sync is true.

Sync Notion pages when None of the following are true:

Should sync (Checkbox) is Not Checked.

This will exclude items that don't have a project set.