In short, this is something that does not immediately affect you, and it should be forwarded along to the author of the addon that is mentioned in the message:
We added this warning because with Season 1 in Battle for Azeroth we made changes to the internals of how the RaiderIO Addon works. This change necessitated deprecating some older functions that we had exposed for Addon developers. This means that the way other addon developers were calling the RaiderIO Addon will be removed in the future. The deprecation warning is there to alert the Addon developers of the problem, so they can update their Addon now, so it won't break in a future build when we remove the functions altogether.