While it doesn't eliminate the 100 item limit, this mod has added some recipes that allow for massive conversion of materials.
instead of needing 1 you need 100 of specific items to activate the recipe.
It gets around the limit quite nicely.
http://www.newvegasnexus.com/downloads/file.php?id=37620
Ironic, but that's the exact same mod I'm using.
You're right that for some things it does work nicely, the problem is, he didn't do that for the majority of what's there. Only about a third of the options are need 100 items to make 1, as you put it.
It's so annoying that making one item causes an exit from the menu!
(PS I like that mod except it's difficult to find pistol powder, and it can't be crafted). Which I guess balances it neatly enough.
Maybe someone could change that.