Well, possibly many of the Baltic peoples were not happy with the unification with the USSR, but actually an invasion by Nazi Germany was anticipated and the governments had to choose between the two evils, as they saw it, and choose the USSR. It is known that Roosevelt during the war asked Stalin to repeat the unification referendums in those republics after the war, because the pre-war referendums were influenced by the immence threat by Germany. Stalin rejected this proposal, saying that the pre-war referendums legally valid even if they were made in a difficult international situation.
So it is possibly true that the majority of those people did not like the idea to join the USSR for ever very much, but it is also true that they made their choice between Germany and the USSR in the pre-war situation. They possibly thought that Germany will not be bold enough to attack the USSR and that they would be able to leave the USSR after the world war is over.