Unlike browsers like Firefox, WebKit based browsers lack a feature "click-to-activate" for plugins. This is an important lack due to its impact on usability and security. This issue was raised in GNOME's Bugzilla for component epiphany, see https://bugzilla.gnome.org/show_bug.cgi?id=172652. According to a developer of GNOME Web (https://bugzilla.gnome.org/show_bug.cgi?id=172652#c16), this issue cannot be dealt with inside GNOME Web but needs to be addressed in the WebKit backend.
The WebKit version is 2.14.3.
Support for NPAPI plugins was removed in https://trac.webkit.org/changeset/265753/webkit.
<rdar://problem/96044670>