You can use the is_multisite() function to test to see if you’re installed in a Multisite-enabled site. That way, if there is any functionality you need to provide specific to a Multisite installation, you can do it like this:
if( is_multisite() ) {
// special code here
}
Most plugins that I’ve written at work, for our Multisite environment, don’t have anything special defined for the Multisite environment.
Additionally…
I downloaded your Document Gallery plugin to a multisite installation I’ve got set up for a project I’m working on. When I Network Enabled the plugin — ie, enabled it for every site in my multisite installation — it remained visible in the Network Admin > Plugins section, but not in the individuals sites’ Plugins sections.
When I Network Disabled it, it then reappeared in the individual sites’ Plugins sections. I was then able to enable it for individual sites.
When I Network Enabled the plugin, the [dg] shortcode was available for use. When I enabled it on an individual site instead, the [dg] shortcode was available in that site.
This is the behaviour I’ve always seen from Multisite, which I’ve used at work since WP Version 3.0.
Your user might have encountered a plugin conflict. All I can report is that your plugin works as expected on my WordPress 3.5.1 Multisite installation.