Ever since he was little,Nagisa had been good with girls.Not in the sense that he constantly received confessions and flirted with them,but in the sense that they liked playing with him and didn't feel anything negative towards him.Since the first year of middle school,some girls had expressed their feelings towards him,but he always politely declined with a smile,and if asked why,he would simply reply 'I'm not really interested with girls'.They still enjoyed being around him,though.
There were always rumours about his sexuality going around.'Nagisa is gay' this and 'Nagisa is gay' that.After a while,they died down because it was,well,not a rumour.If someone asked him upfront,he would say that he was gay and had been since he was thirteen,so it wasn't really a rumour,it was the truth.Since the 'rumours' stopped circulating,the word never hit some,namely Rei.
Just because he would tell his sexuality did not by any means imply he would be as open about his crush.The girls would giggle with him,pleading and begging for him to fess up,but he was sealed tight.But he had been in love with that person for two years,and leaving subtle hints.
I think you can guess who his love was.