Show "Settings" link only for enabled plugins
I think it will be good to hide settings link for disabled plugins, because some plugins "runSettings" action can't work properly without overrides (from this plugin) for onBeginRequest
You need to be able to change settings even if the plugin is disabled. It should be a simple page for basic settings. What kind of overrides do you need in onBeginRequest for the settings page?
At onBeginRequest I importing custom models, checking and adding to database nonexistence settings. Of course I could duplicate this code to the runSettings function, but i think it will looks strange.
Changing the settings of disabled plugin - seems strange to me.