Looks like all input tokens, except for special tokens are masked.
So, yes the second sentence will have tokens masked as well, but not the [SEP] between it and the first (and the other special tokens).
Why I think so:
Looks like probability_matrix is just a tensor the shape of (all) inputs, filled with the 15% probability of being masked…, except for the special tokens where are set to have a 0% probability of masking before being passed to torch.bernoulli here:
  

      github.com
  

  
    huggingface/transformers/blob/master/src/transformers/data/data_collator.py#L379-L380



      
      
          probability_matrix.masked_fill_(special_tokens_mask, value=0.0)
          masked_indices = torch.bernoulli(probability_matrix).bool()