Some operators/countries do not provide the appropriate timetables so their services do not appear in the planner.

The interrail app/planner is not a reliable tool in general due to the way it receives only occasional timetable updates. You should use other sources for planning your trip.

The planners of the likes of bahn.com and oebb.at are recommended for most countries, it is always a good idea to look at the websites of the local operators as well.

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

I should add the quickest direct non-flying route from Stockholm to Tallinn is by ferry not train, several operators serve Sweden - Estonia, some, Viking and Silja-Tallink offer discounts for passsholders, see benefits section of interrail app for details.

It MAY even be cheaper/more trips to go via HELsinki or Turku-plus the chance to see a bit of FI-perhaps even NOkia!

Also note that-assuming you will not stay in Tln forever and want to go onward-even by train, that this is via the 3 baltics not a very good way to go. Trains are sparse, as EE also not listed and in LV and LT quite cheap. Read seat61.com for best overview on what is available for overtheborder.