in a not so toungue in cheek suggestion ...
WHEN you pull the carpet (you will pull it to paint it right?) ... scrape off the "padding" since that's the sponge that holds water and promotes rust. Also, scrape free what's stuck to the floor as well. Then you can see if the floor is showing signs of rust. Any surface rust spots you see, wire brush it down good, and spot spray that with a rust inhibiting paint.
Up to you what to reinstall (it's your rig so your choice).
I've done this on 2 different rigs (both got herculiner). On one I cut the carpet to simply cover the tunnel between the seats, but left the floor with the herc, and then added rubber mats. The other is just herculiner at the moment, but I think I'll add some "truck bed rubber mat" cut to fit nicely.