As far as seat reservations, hard to say, They are only 3 EUR pp when you buy at www.oebb.at. When you arrive and know which train you will be on, you can check the projected loading at www.sbb.ch/en.
Keep in mind that the train will change directions at Buchs SG, the last station in Switzerland. Zurich to Buchs, be on the left hand side of the train for views of the Zuerichsee and the beautiful Walensee. After Buchs, you will be on the right hand side of the train. Look out the window. You're in Liechtenstein. Cross that one off your bucket list. The right hand side is the best for the view of the mountains as the train climbs to the Arlberg Pass.
If one of you is squeamish about traveling "backwards", get seats facing each other over a table. Then you can switch when the train changes directions.
PS, you can take the first available train from Zurich Flughafen to Zurich Hbf. The Railjet to Salzburg leaves every 2 hours. There are plenty of shops, restaurants, cafes at the Hbf to kill time waiting for your train to Salzburg (unless of course the timing ends up being quick).