Is there any way to do height based media queries in MUSE (or Dreamweaver for that matter)?
You can add any custom CSS stuff in the published files using whatever editor you deem suitable, including Dreamweaver. Just be aware that height detection is notoriously unreliable and will still be overriden by other rules that take precedence, including width as defined by the Muse breakpoints.
To add to what Mylenium has said.
Detecting the height using a media query only detects the screen height and not the page height, which leads me to my question -
why, if i may ask do you wish to do so?
I can see it being of value in trying to make a layouts elements proportional to the devices height available, (for example you do not wish the header to take up too much of the screen height available), but it may help us advise you better if we knew what it is you are doing that would make the screen height so important.
Note: if it is to set the height of say a lightbox, then consider using 'vh' values, (vh = vertical screen height in %) to set the height of the lightbox, and its width equivalent = 'vw'.
The 'v' actually stands for viewport.