We would like to remove this plugin. Does it have any affect on emails notifications or is it just something extra? without this plugin, would JIRA be able to continue sending emails notifications as usual?
It's an extra function. The notification schemes send emails when events are caught. The "email this issue" plugin allows users to click "send this issue to someone" without an event being fired.
So, as you are already thinking, yes, they are separate functions and turning off the plugin will only stop people clicking "email this issue", notifications will continue to go out on events.
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