The shader system should be converted to the same system that armor and weapon mods currently run on. When you get a shader for first time, it's permanently unlocked and in your inventory, When you want to apply it, you just pay a small amount of glimmer.
I don't think anyone enjoys the laborious task of deleting huge stacks of shaders. This has been a problem since early D2, and I think the new mod system is a good template to fix it.
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Just combine D1 with D2. Allow 9 shaders at a time (like emblems). Make them infinite use, and when you want different ones, you just stow them and unlock others from your collections. Simple