They can be contributing to a low KH? Wouldn’t those things raise it if they are affecting the water at all?
You are correct. However, I thought you were trying to determine what is causing
the KH (and GH) to rise. In order to identify those, you will have to go through a process of elimination. The shells are likely the KH component, but may not be all of it.
If it were me, I'd pull them all out (not the substrate), get the GH and KH levels down to half, or less, then wait a week to see if anything changes. If no changes, then add all the rocks back in and wait a week. If no changes, then add the shells (if that is what you want to use to raise KH), then wait a week. If you get any changes at any point, then determine what is the thing that is causing those changes.
If you want to test the rocks, individually, when they are out of the tank: put each rock into a different bowl of tap water, then add some lemon juice to make it acidic. Test the water and then test again after a few days to see if GH, KH and pH change.