eM Client can automatically find duplicate items in your accounts or local data. The tool that helps you do this is called Deduplicator.

Open the Menu > Tools > Deduplicator.. section. In the window that pops up, you can choose if you want to run the Deduplicator tool on your emails, events, tasks, or contacts. Select the item type, and click next.

You can choose to search either in individual folders or in groups of folders. Make sure that you select the folders/accounts you want to be deduplicated. Otherwise, you will receive an error message and will not be able to continue. Once you have selected the folder(s), click next.

In the next step, you can choose the action to be performed with the duplicates - either delete them permanently or move them into a specific folder. If you want to sort our the data and double-check before you remove it, sorting them to a custom folder first might be a good idea. 

Then just let eM Client find and take care of the duplicates for you.