The head gasket will not affect the rocker geometry. Since they are shaft mounted, the height of the stands are the easiest way to control the rocker geometry. The length of the valves and their depth in the heads will also affect geometry, so if you're dealing with a rebuild, those are other variables.
If you don't know how the geometry is and you remove those trays away, you have changed the geometry and you don't know if it is a good or bad change.
What the thicker head gasket will affect is the geometry of the pushrod between the lifter and rocker, but I think that's just something you have to live with. It will also change the position of the adjuster screw in the rocker arm and you will loose a bit of the rocker ratio.
So if all that is changed is head gaskets, you will loose some valve lift and duration because of the lower rocker ratio. You also lower compression. If you throw away the baffles, the rocker geometry will change and is questionable if you did not check so you can gain or loose something there.
Not all shim or composite gaskets are the same but a good general number for the difference in thickness when torqued is probably about .020"
Bottom line, if you are actually trying to gain something, composition gaskets alone are not the way to go but they are fine and probably best for an engine that is in service and needs only a head gasket. With rebuilds, the block and heads are usually milled and that usually makes up the difference in the thickness of the gaskets. They will not change the rocker geometry.
Lawrenceville, GA