It should be there. Can you post a screenshot showing it missing?
What operating system and version of InDesign?
You could always reset your prefs and roundtrip your document through IDML...
You can only ignore the position in the Character Style dialog, not the basic character formats section of the Paragraph Style dilaog, presumably because you must define some position for any any text, and the basic place to do that is the paragraph style, while the character style is used to override the previous definition, and you might not care about any particular attribute when overriding.
How was the superscript applied? If by character style, you would need to either create a second style that also includes the superscript along with any other feature you want to add, or use a GREP style to add additional overrides -- that's currently the only way to apply two or more character styles to the same text.