1) If I write a PHP script to add the users directly to the MySQL dB, what other tables need updated at the same time to keep everything in sync for CB?
Direct database additions of users can be dangerous. I won't even recommend what tables. Please use CB Juice to mass import users via CSV files.
2) If, instead, I manually add each user through the Backend, is there a way to delay the automatic email until some time in the future?
Only way I can think of is to edit Joomla global configuration mailing information and set it to something invalid like Send Mail with a path of "NOT-VALID" this would prevent the email function from working as of course details are invalid. Once done adding users you could change back to valid details.