People think Johnathon knows Will is gay is because 1)Wills speech to Mike about how his feelings towards losing El shouldn't be the reason he loses El. Johnathon keeps looking in the review mirror at the two, but to me, it seemed like Johnathon took Wills words and applied it to Him and Nancy since Johnathon as expressed the same concern that Will is towards El.

2) Johnathon telling Will that he can talk to him about anything. Will says "When you're different, sometimes you feel like a mistake". This can apply to s1-2 since those are the scenes Will has to have everybody over his shoulder. He feels as though he's a burden to everyone around him. Johnathon obviously notices this and his telling him that he's sorry for being an ass of a brother and wants that relationship again.

3) Recently, people have been noticing in s3 when Mike does the "I love her and i can't lose her again" speech. Johnathon and Will look at each other. But i mean. everybody was shocked. I don't even think Lucas and Max used that word so of course, everybody's looking at each other, speechless.

Nevertheless, i don't think anyone really knows Will is gay, i don't even think Will knows his gay. It would be cool though if in season 5 we get a guy love interest for Will and see how he handles it. Let me know what you guys think and if i missed anything