Are there long-term effects of bile duct diseases?

Yes. And they can range from the simple (stones, changes in bowel habits) to the serious (cancer of bile ducts or liver). Luckily most are self limited and don't have long term influence in survival.
Bile ducts. Depends on what you mean by bile duct problems? If associated with gallbladder there are one set of potential issues. If associated with the liver there are set of problems.
Too broad. Question is too broad. Specify the condition. Usually biliary diseases are complex.

Related Questions

I live in a college town with many healers who use Asian treatments. Will they work on bile duct diseases?

Standard. I can't recommend since I am not familiar, but be careful. Bile duct disease should be taken seriously and care for promptly. Make sure you see a traditional doctor before trying unproven methods.