Viewports in Layouts are just windows looking into the modelspace area.

When you change the modelspace layers settings, all the viewports are affected: that is what a window does, it simply shows you what is on the other side.

What you need to do is thaw/turn on all the layers in modelspace and work inside your viewports instead: or get in the habit of turning on/thawing all layers in modelspace when you are done working there before you go back to your layouts/viewports.