Hi,
You will have to unregister the Softaculous app also from the server, so it will not appear in the WHM.. Use the below command:
# /usr/local/cpanel/bin/unregister_appconfig <app_name>
In addition, if the above does not work, use the below steps:
# cd /var/cpanel/apps/
# /usr/local/cpanel/bin/unregister_appconfig /var/cpanel/apps/<softaculous_config_Name>.conf
# rm -fv /usr/local/cpanel/whostmgr/docroot/cgi/<softaculous_app_name>.cgi
# /usr/local/cpanel/bin/update_appconfig_apps
Replace part of it with proper configuration file of the app you want to uninstall..