Update:
There are now settings for changing the header height and logo margins in the Site Design Settings.
If you are making the header larger, the logo will currently appear with low resolution. Copy and paste the following code and add it to the Custom JS field in the Site Design Settings. This will then use the originally uploaded image size.
JS for hi-res logo
var logo = $('.logo-img')
var src = $(logo).attr('src').replace('/s/', '/').replace('/l/', '/')
$(logo).attr('src', src)