I've been fragging all the quest and ornament stuff I've been getting since the last Crystal Shop restock (a week ago) and I just barely have 10,000 crystals. The slow method is not effective when higher priced items like the two books that were over 10k are released with such a limited amount.
I think that a higher denomination would be helpful. At least then if I really wanted the book, I would have a chance at getting at least one copy. Now, I have none, and it took me a week to get to the point where I could even have purchased the cheaper one - but of course now there are none.
I also really like the idea of them looking slightly different from the singular denomination. It's like that for the wizard tokens (which come in denominations as high as 1000, btw), so why not?
Here's the thing too: unlike wizard tokens, you can't "cash out" crystals. Even if higher denominations were implemented, once you've turned them in, you can't take them back out again. So I think that might help keep them from flooding the market too much.
[Edit]Just wanted to add, kinda relevant to the season, but having higher denominations of these crystals would make it easier to gift them as well.