I am using LyX, and I was wondering if there is any ERT Command for automatically inserting wordcount in a document? I am on Windows.
Lyx has the same problems LaTeX has to give you a proper word count. The reasons you can read in the question is-there-any-way-to-do-a-correct-word-count-of-a-latex-document (as @cgnieder said in his comment).
So the best way seems to me to prepare a PDF with Lyx and count there the words.