The Superscript sub category currently has the following requirements set.
name = Superscript;|
predicate = subCategory == \Superscript\ AND category == \Letter\;|
Due to this only glyphs that have their category set to Letter and subcategory set to Superscript will appear there.
The issue is that no generated glyphs seems to fulfil these conditions by default without manually changing a glyph’s parameters or using a custom glyphsdata.xml file.
The latin and cyrillic modifier letters such as amod and amod-cy are has their subcategory set to Modifier by default instead of Superscript. Changing it to Superscript in the glyphsdata.xml file causes them to correctly appear in the Superscript sub category.
.sups glyphs derived from modifiers letters have their sub category set to the same value as the glyphs they are derived from.
.sups glyphs such a.sups or a.cy.sups have no default category by default, even if they should likely have it set to Superscript or something similar. The same is also true for .subs glyphs and the missing Subscript sub category.
The only issue with giving .sups glyphs a Superscript sub category is that superscript modifier letters and .sups glyphs would be placed side by side in the default glyphs view instead of in different “lines” as they are currently.
What I am not sure of however is what the Superscript sub category was originally made for. Was it meant to house superscript modifier letters, .sups superscript glyphs or both?