In 2023, Baseball Reference made an update to historical franchise nicknames on the site. Changes were made based on the most commonly used name for teams in their home cities, while prioritizing official team nicknames where applicable. In some cases, teams were known by no nickname at all and went solely by the name of the city they represented.
Full details on these updates can be found in this blog post:
A notable change was the nickname for the original American League ballclub in Washington. For much of its history the club's official nickname was the Nationals, and this is now reflected on the site for the relevant seasons.