I've long been frustrated with database query tools like pgadmin 4, Microsoft SQL Explorer, etc. There are quite a few reasons, not least that they don't really give you tools to deal with the reality that your tables form a graph and your rows form a graph (e.g. you should be able to see the user record plus records that are effectively part of the user record as a graph on one screen) but the other one is the one you mention, that they just don't integrate with version control and the way people use SQL in code (e.g. maybe you should have *.sql files with your queries but practically people spray SQL all through their PHP, Java, Python, Ruby, whatever they are coding)
I think the most disciplined organizations use stored procedures but the ordinary methods people use for managing those often date from before version control. (e.g. so many people would wrongly laugh at stored proc users for being so 1990s + Oracle)