Helen knew about the project before she died- did she never find out that he was the one that got frozen? If so, why didn't she try looking for him to unfreeze him?
~"Hope is a good thing, maybe the best of things, and no good thing ever dies."~
Helen couldn't find him the next few decades because either the Government did not declassify the experiment on Daniel or that she assumed he died in the warehouse fire were Daniel was kept, the one that claim the life of his friend Harry who was trying to save him from the fire.
That's my guess...
I can't remember, but I think Harry died before Helen awoke from the coma. He couldn't have told her about it. Even if someone else did, she might've assumed Daniel died in the fire that killed Harry like you said. Also, I don't think she knew all the details of the experiment and since she wasn't military, they wouldn't tell her anything about it if she asked.
Tomorrow's just your future yesterday!