I'm not sure. I know when I had mine it nagged and replaced them when I wanted eshop.
I know I put them back after I was done with eshop and can access eshop now still. However, there was a period of a few weeks between me accessing eshop again and I have updated reinand several times.
Perhaps something in the updated reinand allows it? Perhaps eshop updated my firms again and reinand itself is patching them instead? Hopefully someone else with more knowledge chimes in.
For now if you need to get on eshop go ahead. just put back your custom firms when done?
It could be because your console checked in with ninty servers and sees that TWL/AGB are on older versions and prompted for an update. You can remove the update by holding the button combo during boot (forget what it is atm), and also block the update servers in your router which might let you back into eShop since your nver is on the latest version.