I always thought Ennis knew it was love. He tells Jack that the reason he dry heaved was because he never should've let Jack out of his sight. He refers to Jack as "little darlin'". He sacrifices his financial welfare and family to keep his flexibility for Jack. The idea of another man with Jack enrages him with jealousy. I don't think that Ennis didn't realize his love for Jack until it was too late. I think he didn't realize that he was willing to take the risks until it was too late.
He didn't figure that out until a year later, probably when Junior was born, and he wish he could share the good news with Jack.
Altough he knew it was special, like the reunion thanking heavens, but I don't think he knew it was love, the kind that lasts a life time, until Cassie told him girls don't fall in love for fun. Then he realized that in spite of all the hardship, quit jobs, hiding, lying, losing his marriage, the life with Jack was still better than life without him. That's when he could put a name to this thing with no reins.
Up till then, he was just trying to figure out what's wrong with him...a regular guy who wouldn't pay no attention to another guy, and who kept wringing it out hundreds of time thinking of Jack.
I don't think Ennis was smart enough to figure it out on his own. No offense Ennis. Just that, feelings get too confusing for anyone to handle on their own. Ennis was lucky to have Cassie and Jack's Ma to help him along when he needed help. Junior, I think, will be there for him when he gets older, like in the short story.