Yes, they will automatically be using greybox after the upgrade, like it or not ;-)
I will probably leave the ibox files in place in case people are using it in custom features. For example in the mojoPortal.Web.Controls project there is a HelpLinkButton which uses iBox and I'm afraid people are probably using that in their custom features. I have recently marked it as obsolete/deprected because I've changed all the help links in the mojoportal features to use the new mojoHelpLink located in the Controls folder of mojPortal.Web project, it also uses the new greybox instead of iBox.
So basically I'm no longer using iBox for anything in the included features of mojoPortal and don't plan to use it going forward, but will leave it there for backward compatibility with other custom features that may exist in the wild and still depend on it.
I've seen tons of stuff on Codeplex for Flickr, its probably really low hanging fruit to implement it using one of the helper libraries out there. One day I'll get to it or maybe someone in the community will do it first.