Thanks John, this makes a lot of sense.
I just went to Home > Security > Certificate Usage > clicked RADIUS EAP > and changed the cert drop down box for Authentication To The Peer to be: Dummy RADIUS Server Certificate, and down below that I went to Peer Authentication drop down and changed it to Dummy RADIUS Authority and clicked Save.
Then I went one tab back to Certificates Store, saw that the expiring ones no longer had anything used them, and clicked the trashcan (bin for my UK friends :-) icon and now all my icons are green and no more annoying warning.
I just disconnected a wireless client from the network, made sure the controller no longer saw it as connected, turned wifi back on, connected to wifi and everything is working great, so for anyone reading this down the road, you can rest easy that this shouldn't affect your end users, unless of course you actually are using RADIUS 802.1x authentication from client to AP/controller.
Thank you everyone,
Squelchtone