Were Czech and Slovak languages already considered two separate languages when Czechoslovakia was united?

Answer 1

Yes. Both Slovak and Czech languages (among others) likely originated from archaic Slavic language Proto-Slavic spoken during the Great Moravian Empire. They started to evolve and separate in 10th - 11th centuries.

Czech and Slovak are closely related to the point of mutual intelligibility.

Answer 2

As far as I know, the Czech language and Slovak language have always been two languages. Czechs and Slovaks understand each other without difficulties, especially the older generation, for nowadays children it can be different.