They don't disable, because they cannot. S&D will not put addons into stadby either, because that state is saved on logout. If you really want to unload your mods after you leave a raid, reload your UI.
Addons need to define specific fields in their TOC for S&D to even look at them. Most addons outside my own don't use S&D yet, because everyone's afraid of the dependency :P
I bounced the idea of "conditional LoD" off slouken right after I wrote S&D... basically it would allow you to define the addon's stub. If the stub is present, the addon is LoD. If the stub is not prosent, then the addon loads normally. Essentially tying OptDeps and LoD together.