Is it a best practice to exclude retweets from the data set?
No. I do not believe so and I can explain a few reasons why.


If an entity wants to create waves in twitter with false tweets retweets are probably apart of the plan.
If you want to detect tweets generated by bots looking at the statistical data on said tweets and retweets like time stamps could be relevant to detecting if the tweet is generated by a bot.
If You have a way of checking retweets by bots then removing all retweets would also remove that data. 


You should remove retweets if. 


The project is focused on analysis of text to determine if a tweet is bot or not.
There is no labeled human or bot retweet data.