I would like to know if anyone in this forum knows of any software which can accurately help me calculate the noise levels in a multistage orifice after the pressure drops in each plate?
I doubt such software exists in the form you ask for. This is just a suggestion as an alternative: download Fisher Catalog 12 to get the theory of generation and propagation of noise, including how to "add" the noise produced from each stage. It isn't clear if your interest is in aerodynamic or hydrodynamic noise, but the information in the catalog will give you a basis for making a calculation. This will tell if you are likely to have a problem, and give some suggestions to mitigate.
For software based calculation your best bet maybe to use control valve software for a globe valve of similar port size- i.e. a valve which has poor pressure recovery characteristics similar to an orifice plate.