But nobody is alleging that they did all the work in perfect secrecy. Clearly we know about a lot of the work: you'd use the same equipment, location, and so forth. Only a few things are left that need to be secret; namely, the origin of the viral sequences that preceded SARS-CoV-2. And if those were present in the wild it seems not entirely surprising that WIV could have simply obtained them.
Furthermore, it is not really that surprising that research which potentially develops weapons of mass destruction is kept secret, pandemic or no. Whether it caused the pandemic or not, people are still generally concerned that this kind of thing was occurring.