Any material that is not natural alters energies. That goes for things in your house, clothes, and also orgonite.
You'd have to tune into a crystal to know whether it's okay with orgonite or not. Another question is, are you?
Personally I'm not a fan of it. Some items look pretty, but that doesn't mean they exude an energy that's beneficial.
Someone makes it, hopefully / likely with the best intentions, and they may think it does a good thing, but what someone thinks isn't always correct. We are mostly still driven by the head.
Nature doesn't create that way at all.
As I'm not a fan, and had a not pleasant experience with orgonite, I'd be inclined to say that crystals aren't happy inside it either. They can't do what they normally would do, and can't give off the energies they could and would when still 'free'.