If they want it out I think 2 inches won't be much of a barrier, but it can't hurt.
Some people use a piece of carpet or shelf liner in the bottom of the nests.
Are the shells fragile?
I found it fascinating when I read that hens stand when they lay. Had never really thought about it.
Imp
Could just be new layer issues.
Your thoughts are good and I'd start with the easiest options. I think a softer landing for the eggs would be my first project.
Here some other ideas:
Hope this helps
http://www.thepoultrysite.com/publications/1/egg-quality-handbook/14/hairline-cracks
There...