I know that manga publishers such as Weekly Shonen Jump hold character popularity contests for mangas such as Naruto and Bleach. Where did this originate and why is it done?
This is such a common marketing strategy that I doubt it has an origin, but as for why it is done, it is to cater to the audience.
In the manga Bakuman, a popularity poll placed a side character named Kazuya Hiramaru in fourth place, immediately afterwards several chapters were devoted to him, which were very popular.
This implies that this practice is equally beneficial, and probably smiled upon by both readers and editors alike.