The only choice of applying prefixes and suffixes is to either one, or both, reference and note number. Nothing in there to specify one format for one and another for the other.
An ugly way could be to mess around with the Note paragraph style and try to get rid of the leading space. However, a quick try shows that this is a regular space — it grows and shrinks with the others on the same line. You could make it a non-breaking fixed width space …
(After some fruitless tinkering) Best is not to rely on ID’s automated systems, then. Set the right prefix and suffix for *one* of the two, and add it for the other as regular text.
If you use Prefix/Suffix for the Footnote References and your footnote text always has the same style, you can easily use Find/Change to add the parentheses around the number:
* add parentheses around the footnote marker
* copy
* in Find/Change, search for ^F in your footnote text style
* replace with ^C