In the assembly mass of each part is added automatically by the software.
So mass of your assembly is what comes out from adding all your parts.
As far as I remember when you cut the assembly (extrude in assembly environment) mass is not updated based on this cut and it actually stays as per assembly without any cuts.
This operation most likely only removes parts of the geometry from rendering, and as assembly is a rigid body environment it calculates mechanical properties based on global properties of the parts (most likely).
What you can try (I did not) is to execute this cut in "Machining" environment of the "weldment" type assembly.
This potentially may have different result than for cut done in modelling environment of standard assembly.
(interesting BTW, I need to check).
Cris.
Cris,
https://simply.engineering