I normally use expertflyer when I want to get an idea of flights on a route on specific dates. It also gives the seat availability etc. Here you can also setup alerts when seats become available.
I have wondered about the missing flights on the SK booking site too. As far as I can see. If there are no connections the flights disappear when they are sold out. If there are connections they stay there.
The reason the flight came back with seats available in all classes could be because they switched to a bigger plane.