How can I have network sites not use year/month folders by default?

When creating a new network site, by default the site option Uploads Use Yearmonth Folders is on (set to 1). I have to set it to 0 each time I create a new site. This isn’t horrid, but is it possible to make this the default for newly created sites? Perhaps a hook or something I am overlooking?

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You could just change the option after the blog is created:

add_action('wpmu_new_blog', function($blog_id){
  switch_to_blog($blog_id);
  update_option('uploads_use_yearmonth_folders', false);
  restore_current_blog();
});

Drop this code into a .php file inside wp-content/mu-plugins

I’m a little confused by your question. Are you referring to URLs? If so go to Settings > Permalinks and adjust from there.