If OP adds 3311 emojis to the vocabulary, then you’d expect that the probability vector for the mask token in Are you happy today <mask> includes probabilities for all the original tokens of the model as well as probabilities for all the 3311 emojis.
OP seems to suggest that the output probabilities for <mask> do not include probabilities for those added emojis, i.e. the output probabilities do not have the same size as the vocabulary size. That is at least what I understand from OP’s post.