Have you tried using the Deutsche Bahn planner? Also available in other languages. Like I mentioned earlier (on Facebook, I believe): via Germany and Austria and avoid Thalys.

As to prices: the cheapest Interrail for -28 is a 4-day/1 month pass, normally EUR 185, now EUR 167.

Can we use the interrail pass for all these routes? And if we for example leave on the 31st of august and we arrive at 8 am in Zagreb, does that count as one trip on the interrail pass or as two trips and is this different if we need to change trains a few times? I was also wondering if we would need reservations for most of the trains or if we can just take them. If we need a reservation, does this cost extra?

The Nighttrains on your route would need a Reservation you have to pay on top of the Railpasses as you arrive 8am i assume you intend to catch the Munich - Zagreb nighttrain :)

As the train departs in Munich before midnight and goes directly to Zagreb you need only one travelday to get to Zagreb :)

In the case of going back to Belgium like Zagreb - Nighttrain - Munich - ICE to Belgium you would need 2 traveldays as you change trains after midnight 1st Travelday Zagreb - Munich 2nd Travelday Munich - Belgium

Other option to get in one travelday back to BE/NL from Croatia to Vienna and catch the Nighttrain to Brussels or Amsterdam :)

You can catch the nighttrain to Amsterdam also in Munich. 

Please note, that the nighttrain Munich-Zagreb only runs only on some periods of the year.

→ take ICE Brussel-Frankfurt and Frankfurt-Munich(no reservation needed) and than change in Munich on the EN to Zagreb (compulsory reservation for Sleeper and Couchette and for seats 100% for Munich-Salzburg and I think you can take without reservation between Salzburg and Zagreb, but I recommend a reservation. Reservation should be available via tickets.oebb.at, interrail.eu or B-Europe(??) office. 

Every day you can take the nighttrain Zurich-Zagreb via Feldkirch. You can catch this nighttrain in Zurich -> take ICE Brussel-Frankfurt and Frankfurt-Zurich (no reservation needed) and EN to Zagreb (reservation needed for sleeper or couchette. For seats, I’m not sure, because it’s not an global-price train, it should be possible to use it without reservation, but I recommend a reservation (via tickets.oebb.at, Interrail.eu or B-Europe(??) office.) 

Nighttrain Zürich - Zagreb is till Schwarzach St Veith reservation compulsory
From there a seating coach will be added and the train operates as a Standard Fast - Train (more coaches will be added in Villach)

Munich - Zagreb is reservation compulsory on the entire Route :)

Here a page with the reservation cost´s you can expect (The Nighttrains can be reserved via oebb.at)