Nope, both mods will remain separate. You can however play AoA and even retail FS2 campaign without any issues when you have WiH selected as mod. Certainly there have been some tweaks to retail ships and weapons, but nothing that should break retail missions.
Merging the mod dirs won't be officially supported, doing so is at your own risk. However, it's piss easy to do. Just rename vp-files so that bp2 vp-files are alphabetically before bp1 vp-files. Doing that has no benefits for you though and I don't recommend doing it. Especially when you're in need of troubleshooting help, your own customizations will play against you.
