Countless times I've come across bathrooms wrecked by water ingress behind the tiles through the cracked grout or failed Silicon. For your peace of mind waterproof the wet areas or if you're boarding up new use tile backer boards which are totally waterproof
I'm afraid this is a complete redo. You can board new with plywood and overboard with 6 mm Hardie boards. Make sure you seal all the vertical and horizontal using good sanitary Silicon
Could be the laitance hasn't been mechanically removed prior to tiling.
Laitance is a weak, easily-crumbled layer on the surface of concrete, consisting of cement and fine aggregates that rise to the surface when too much water is added.
Firstly Hardie boards are water resistant not waterproof which means they they won't get damaged by water but they can let the water get through and damage the walls behind. For boarding around wet areas the best option is so called tile backer boards Wedi type. Hardie boards still need painted...
Don't worry about scratching the waterproofing paint. Just don't apply to much pressure when you trowel the adhesive. The paint is strong enough to withstand the normal trowel pressure.
Better use Wedi boards instead Hardie. They are totally waterproof and you only need to use their special adhesive sealant between the joints. No waterproofing paint and no tape required.