On the average player side of things, yes that was the main point of it. /cardex nationality was a temporary measure made while Realms was being developed, and "/realm join" is simply a replacement for that. On the backend, Realms was aimed towards combining functionality which was split between multiple plugins into one, where we can use Realms' API in other plugins for managing regions, who the leader of a region is, and various other things.
TL;dr,
Players will very rarely interact with realms aside from using /realm join <realm>.
The Leaders of Regions should inform their players that if they hadn't previously ran /cardex nationality <nation>, they should instead be running /realm join <realm>.
This functionality is simply for associating with a nation for warclaims, and has no further planned reasoning behind it.
Notes: If you check /card and click the "Click for more.." button in chat and you have a Nationality, that is automatically converted and you will not have to run /realm join
If you run /realm join <realm> and it says that you're in a realm but it does not show in your cardex, make a modreq and request to have your realm association cleared.
On the side which most players will not see, this plugin serves to allow for (moderation at the time of this post) to manage worldguard data such as PROs, give PROs the ability to use the /rg addowner command, view various regions (vassals, etc) under a nation, among others.