Please don't use the rail planner app (or the Interrail website) to plan journeys. It doesn't get enough updates to be reliable.
The best is to check national planners or apps; for international travel, the DB website or DB Navigator app is a good choice.
In addition, not all railway companies (and certainly not all ferry companies) send their data to the European Timetable Centre, in which case you can only find them on their own websites.
From Stockholm to Tallinn, there are direct ferries but since you will only get a discount with your pass, you don't need to have an active travel day and therefore you don't have to add them to your pass.
For ferries with a pass discount, check here:
https://benefitsportal.eurail.com/?categories=1be1ba1c-80f5-4286-b255-3092f0d486cd