It depends on the plugin what will be visible to the end-user after you install or configure the plugin. Mostly a macro of the plugin must be placed into a page (or another area of the UI) at first to take the plugin into action for the end-user, but that's not always the case. For the Navigation Menu plugin, in particular, you have to publish a configured menu version before it is displayed to everyone. Before that, you can configure and preview the menu just for yourself. Another way is to prevent the menu bar being displayed in the header automatically by disabling the option display navigation in header in the configuration of the Menu Editor (another way is to remove the menu macro invocation in the theme/template if you use this method). In general, for every plugin there may be ways to prevent the plugin/macro being visible to the end-user, so you can configure it properly at first. Like for the Navigation Menu plugin, we have to look into every plugin how to achieve that.
I hope this is answering your question. If not, give me another try!