Many people working on it didn't
actually know what the project was. They were only working on a small portion of
it and were not told that it was an atomic bomb they were working on (as if
they'd have known what that was, since there wasn't one yet).
Throw in
the very tight and heavy security on it, both military and secret service, and
the fact that government had tight control over communications going in and out
of the labs (even heavier than the Patriot Act), and there is no reason to doubt
that it was kept fairly secret.
9/11 Troofers are claiming things that
just did not happen and doing so in direct opposition to the vast amount of
proof and evidence that directly contradicts their claims.
It's
different. Very different. Conspiracy theories are intellectual discontinuities.