Hmm. Well, the way a child ever even gets to the point of calling someone Dad (or Mom) is because the adults in her life self-refer that way. If she is calling him by name, it would be because that's how you and he did it when she was little. (In other words, where one person might say to a toddler, "Do you see Daddy over there? Go to Daddy!" you might have said "Do you see Jason over there? Go to Jason!" This would have felt normal to you because he was not your daughter's dad.) And the fact that the other kids call him Dad suggests that you did it the other way, with them. I assume they are his kids, biologically.
The fact that she is hesitantly beginning to call him Dad suggests that she wants to feel the same in the family as her step-siblings. Presumably, she pieced together that there is a difference in her relationship to your boyfriend and your other kids' relationship to him, just from the language cue of [his name] versus "Dad." I hope she doesn't think it means he loves her less; this is probably not how she is interpreting it, but probably she is more than halfway to figuring out that he might not be her dad. So I think I would go ahead and tell her.
The above poster suggested that she be told that her biological dad loved her very much, I think that sounds nice except it doesn't explain why his family wants nothing to do with her. I would not say things you can't back up, and that might hurt her further if it sets up a hope in her heart of a loving family who wants to meet her. I sure don't see anything wrong with her calling your boyfriend Dad; I'd encourage it if he is OK with it. So when you do tell her that she had a father who died, be sure this doesn't come out that since this was true she therefore can't call your boyfriend Dad.
I think I'd tell her with as few words as she needs to be able to understand it. Something like, "Your biological dad died when you were little, you have never known any other parent besides Jason and as far as we're concerned, he is your dad, and you can sure call him Dad if you want."
She doesn't know that he isn't her real dad. She doesn't know any different because she's been calling him by his name for so long. She just recently started calling him dad. I'm hesitate about whether or not I should explain to her now or wait until she's older and can understand better.
If she knows your boyfriend is not her dad, that is more than half the battle. That's why I asked why she calls him by his name. I assume by this that she does know he isn't her father?
In my opinion, I think the earlier you talk to your daughter the faster she can asimilate the situation. My parents divorced when I was four and shortly after my father began dating and got his girlfriend pregnant and ended up getting married. She raised me, and not long after they married I started calling her mom, but my dad had sat down with me and told me if I was comfortable I could call her mom. I didnt see my birth mother while growing up because she moved away and didnt keep in touch. So if you explained to your daughter that she once had a dad who loved her very much but that he is no longer living. But she now has someone else who watches over her, and cares for her. Once your boyfriend makes her feel like she can call him dad, she will grow comfortable and feel included instead of excluded by calling him by his name.
Why does she think she calls your boyfriend by his name?