In the admin interface it is possible to alter setting on a “default”, “website” or “store” level.
Whether or not the module is visible [and configurable] in these is controlled by the modules config file (most commonly saved as “etc/system.xml”)

There are some lines that looks like:

<show_in_default>1</show_in_default>
<show_in_website>0</show_in_website>
<show_in_store>0</show_in_store>

The variables are fairly self explanatory; 0 is don’t show, 1 is show [I have also seen 2 but I haven’t figured that one out yet]