There are a few places where we check document attachment with jQuery.contains( elem.ownerDocument, elem ) (isHiddenWithinTree for show/hide, curCSS for inline style fallback, buildFragment/domManip/remove/jQuery.clone for managing script evaluation during DOM manipulation), all of which fail inside Shadow DOM:

$.contains(document, elem) will return false when elem is shown in a shadow dom.
change to elem.getRootNode({composed: true}) === elem.ownerDocument works.

We should investigate the cost of a remedy (e.g., a Shadow-DOM-compatible isAttached( elem ) function).