This is a very shrewd question. Well done for noticing this tiny detail! If you think about the context of the rest of the scene in Act II scene 1, you can see that it is vital that the major actors are masked: only with this disguise can the merriment of tricking Benedick and Beatrice go on. However, consider what Don John is planning to do. It is vital that he is not mistaken for anybody else. When he talks with Claudio it is important that Claudio knows that Don John is Don Pedro's brother, thus guaranteeing the veracity of the scurrilous lie that Don John and Borachio tell him regarding Don Pedro's intention of marrying Hero.
However, aside from this, I think there is a further distinction we can identify. There is an irony in that Don John, whilst not pretending to be anyone else, symbolised by the mask, still has a "mask" on his face, but one of deceit and treachery. This mask, unlike the others, will only be taken off towards the end of the play. Therefore having him "unmasked" draws attention to this metaphorical mask that hides his true intentions from the other characters.