By default, the "Help Text" area that you can fill for a field in the Edit field form of a content type (or taxonomy, or...) doesn't use ckeditor.
Here is what we can see under the text area:
Instructions to present to the user below this field on the editing form. Allowed HTML tags: <a> <b> <big> <code> <del> <em> <i> <ins> <pre> <q> <small> <span> <strong> <sub> <sup> <tt> <ol> <ul> <li> <p> <br> <img>
How to force Drupal to use a ckeditor?
Note that, I have tried to use
MYMODULE_field_widget_form_alter (which is, by the way, only called from the module, not from the theme) without success.