Several web-services are using queries (http://wiki.vg/Query#K.2C_V_section) to get information about servers by using the query-function. By requesting a query-package, these websites will get a full list of players that are online at the moment (when "enable-query" is true in server.properties).

Spigot implements a function, that is hiding players (Player.hide(...)), but there is no way to hide players from query requests (as far as I know). You can disable sending plugins in this request by setting "query-plugins" to false in the "bukkit.yml" file, but that is the only thing you can change in this package.

There also is something like a ServerListPingEvent, where you can remove players from the regular ping-package but this will also not affect the query-package.

I hope you can remove hidden players from the package as bukkit did with the plugins before. If there is an alternative solution for this problem, apologize for the ticket.