Thoughts are always there. You encounter many thoughts because they are your subconscious thoughts. If you go deeper, your thoughts are almost nil because they are very subtle emotional intentions and ideas that are hard to define in awkward imcomplete human languages.
The fundamental energy likes to associate or flow upon the wind created, especially the ones created by breathing. When you exhale, the energy must naturally flow from root to crown. With the energy aiding your mind in such ways or otherwise, you will be able to reach a greater depth of your subconscious mind.