I was having the same issues since migrating to the iCloud and Lion 10.7.2.
1. I could no longer see my shared disks on my AEBS when outside my own LAN via BTMM.
2. Nor could I use the Airport Utility to alter settings on the AEBS remotely over the WAN.
The first issue I have solved.
Fortunately I have a fixed WAN IP Address.
With "Share Disks over WAN" checked I am able to connect to my AEBS disk over the WAN (ie at a remote site) from the Finder - Command K - then afp://myfixedIPAddress:548
I am then prompted for my password and I can access my disk.
Hope that helps someone who at least has a fixed WAN IP Address.
However, I would really hope that Apple do give us all back the BTMM features for the Airport Base Station and TimeCapsule.