If you wish to exclude your EndNote citations from your word count, you can do this by creating a new style that hides all citations.
 
You can do this yourself in EndNote by selecting 'Edit' and 'Output styles', then 'Create a new style'.  In the new window select 'File' then 'Save as' and give the blank style a name.  Then save it in your EndNote styles folder in your H drive.

You can then choose this output style in EndNote, then also in Microsoft Word.  As it is a blank style it will remove all citations so that you can then do your word count.  We have attached an example of this called 'Word count style', which you can use.