
I suspect one of the big reasons for encrypting the binary is that it contains Steam site information (IP addresses, login credentials) that it needs when connecting to Steam. Thats stuff they could Only protect from us by encrypting the binary, so it may be more a concession to Steam to protect their site information than it is a desire to hide the binary.
I don't know this for certain, but it seems a likely Business reason for changing strategies from Fo3 to FNV.