When I did this:
Furnace: Iron ore > Iron nugget
Blast Furnace: Iron ore > iron ingot
I still got the iron nugget from the blast furnace. This happened in all recipes where the furnace and blast furnace smelted the same item into two different things. Additionally, all crafttweaker recipes added to the smoker outputted no items at all.

Unfortunately you cannot remove recipes from smoker and blast furnace. I'm going to add a config option next update to disable the auto adding of smoker/ blast furnace recipes which will fix the issue of being stuck with vanilla recipes.

Related to #80 (bug) #217 (bug) #232 (request)
Also #65 #116 and possibly #41

I'll add a config option and mention it in the CraftTweaker wiki

wow theres actually a lot of related issues

It's important to note that on the Wiki there are methods to remove blast furnace and smoker recipes. Are these not functioning or bugged?

They're bugged but I'll update with new information