I believe the fact that there were a military application could not be hidden forever. At least POET's financial reports would show the millions once they are coming in, though this wouldn't happen in the next weeks. And if the money's source won't be disclosed, you can guess easily where it is coming from, just because the source isn't disclosed.
However, it wouldn't surprise me at all if a military application would not be hidden but announced technology-wise. Such an announcement could say what the technological characteristics of the involved POET chips are and who the partner is. So we'd know that there is a military application without knowing what it does.
Anyway, I am just guessing.
Andrea