You can use the map_meta_cap
filter to change permissions for each one of the roles on your site, for each element added to your site by WordPress or by a plugin.
To only allow admins to see and access the Jetpack menu, you could paste the following in your theme’s functions.php file, or in a functionality plugin:
function remove_jetpack_menu_page( $caps, $cap, $user_id, $args ) {
if ( 'jetpack_admin_page' === $cap ) {
$caps[] = 'manage_options';
}
return $caps;
}
add_filter( 'map_meta_cap', 'remove_jetpack_menu_page', 10, 4 );
(or even seeing that I’m using it, for security reasons at least)
it’s worth noting that you can’t really hide the fact that you’re using a specific plugin on your site. Plugins often add resources to your site, so anyone looking at the source code would see some of the plugins in use on your site. They could also look for the plugin’s readme.txt file, and they’d get a confirmation that you’re using a specific plugin on your site.
In general, security by obscurity isn’t a great way to protect your site if that’s the only thing in place.
Luckily, that’s not the only thing protecting your subscribers from accessing or editing your Jetpack settings. Indeed, while subscribers can see and access the Jetpack menu in your dashboard, all they can do is link their own WordPress.com account to the site to be able to use features like Notifications. They won’t be able to see what modules are active or inactive on your site, and they won’t be able to edit any settings.
I hope this clarifies things a bit.