1. Naomi and Shanna are currently not planned as squad leaders. However, there are 5 remaining spots for squad leaders in the vanguard forces, that aren't absolutely fix yet. While I have some ideas and names on my list, until those vacant spots get filled, I can still make changes.
2. Even if I started to work on the war system, it'll still take a while before we get to the post-war content. The effect might be different per country, and depending on the choices you made before and during the war, but conquering the country and making it part of your domain would be the main purpose of any war.
3. The events around Begus and the church will continue in the events before and during the war.