It might have given Emma trouble if she had to conceal from Mr Knightley the fact that Harriet was in love with him, especially since her conscience would not have let her begin to distance Harriet (as she does or plans to do in Chapter 55) if Harriet had not become engaged to Robert Martin. I don't think any useful purpose could be served by her telling Mr Knightley that Harriet had once had a crush on him but no longer does. In fact, since Harriet certainly didn't tell Emma about her feelings with any idea that Emma should tell anyone else, it would be a breach of trust. Emma does not tell Mr Knightley everything - for example, she told him she had never loved Frank Churchill, which was true but which she had only just realised herself. I see no sign that she plans ever to tell Mr Knightley that she once thought she was a bit in love with Frank, but had ceased to think so even before she realised she had been in love with Mr Knightley all along. Nor do I think she should do that - again it is in the past and no useful purpose could be served by revealing it.