Rosecrantz and Guildenstern spend almost the entire play in a state of uncertainty. Since the play is absurdist, the constant questioning of the two courtiers, who are at turns knowing and completely ignorant of their fate, the uncertainty is presented humorously. For example, in Act One Rosencrantz and Guildenstern play the ridiculous game of "Heads/Tails" flipping a coin. Though in the real world the outcome of a coin toss is truly uncertain -- there is a fifty-fifty chance it could be heads or tails --when Rosencrantz flips the coin it is always Heads, except for the very last flip that sends them into Hamlet. What does this suspension of chance, or uncertainty, mean?
Since Rosencrantz and Guildenstern Are Dead is a play inserted inside another play of which the ending is known to a great many people (Hamlet), the characters are trapped within a framework in which there is no uncertainty. Hamlet is still Hamlet in this play -- with the same characters and the same unavoidable ending every time. That's where Stoppard's idea of uncertainty comes in. In art, Stoppard is saying, we can manipulate reality so that it is the same every time, like the coin flip, and therefore we can control what the audience sees. Since the depiction, and the audience's understanding, of death is a central theme of the play, it is necessary, within the controlled world of the play, to eliminate uncertainty.
But life, we are continuously reminded, is not like a play. We are uncertain -- we do not, usually, know when we are going to die. We do not know if, when the coin falls, it will be heads or tails. So, within the controlled environment of the play Hamlet, Stoppard has Rosencrantz and Guildenstern question everything, including their own identities. This most basic uncertainty (such as in Act One, when Rosencrantz and Guildenstern first meet the Player, and they are unable to even decide which one of them is which: “Rosencrantz: My name is Guildenstern, and this is Rosencrantz, (Guildenstern confers briefly with him) (Without embarrassment) I’m sorry – his name’s Guildenstern, and I’m Rosencrantz)) is meant to show the human condition.
The clever use of tertiary – but well-recognized and pivotal – characters in one of the most famous plays in the English language is meant to show that we, no matter how predictable or humdrum we think our lives are, are in the same sort of uncertainty that Rosencrantz and Guildenstern are. The illusion of art gives the audience the ability to look at that uncertainty from a distance, and see the absurdity of it.
But as far as a theme of the plot, there is no actual uncertainty for the two characters. There is no doubt in the audience (and The Player's) minds that the end is coming for Rosencrantz and Guildenstern -- their fate is in the title. The uncertainty can be whether Rosencrantz and Guildenstern are experiencing the events leading to their death after they are dead, or before, or perhaps only in the imagination of The Player. This is an added level of uncertainty in the play, but on some level it is for the audience and not the characters.