Are you looking for logo options inside the Header Options of customize ?
If you are using the latest version of WordPress 4.5, and if you are looking this options inside there, you will not get it there. You have to go inside Site Identity to find the logo options. Because WordPress added this functionality on core and we moved this options inside the Site Identity. Due to the WordPress core implementation, we feel necessary and change this functionality inside the Site Identity. To find this options,
- Go to Admin Panel
- Go to Appearance > Customize > Site Identity > Logo
- Upload/Remove the logo from there
- You will find Site title and Identity options or logo options too
- Use the available options and click on Save & Publish to save the changes.