Acoustic stud wall - over laminate flooring or not?
Laminate flooring should typically not be pinned by cabinetry, walls, etc. It needs to be able to move slightly. I would cut a channel for the new wall plate. 

Be aware that many such floors have very hard wear layers. It can be hard on saw blades. 



Update: I now understand that you're talking about a suspended wall, or perhaps just furring strips on the brick. In that case, it's fine to run the flooring underneath. However, I'm not sure even acoustic caulk is flexible enough to prevent problems. I'd probably use foam rope caulk--something that isn't actually bonded to either the wall plate or the flooring.