Generally speaking you can divide a database into two broad categories:
OLTP Systems
Online Transaction Processing Systems are normally write intensive i.e. a lot of updates compared to the reads of the data. This system is typically a day to day application used by a business users of all scopes i.e. data capture, admin etc. These databases are usually normalized to the extreme and then certain demoralized for performance gains in certain areas.
OLAP/DSS system:
On Line Analytic Processing are database that are normally large data warehouse like systems. Used to support Analytic activities such as data mining, data cubes etc. Typically the information is used by a more limited set of users than OLTP. These database are normally very denormalised.
Go read here for a short description of these and the main differences. OLTP VS OLAP
Regarding your INSERT/UPDATE/DELETE
point go read about the MySQL ON DUPLICATE KEY UPDATE
statement which will resolve that issue for you easily. It is called a MERGE
operation in most database systems.
Now I dont understand why you are worried about JOINS. I have had tables with millions (500 000 000+) rows that I joined with other tables also large in size and the queries ran very fast. So designing a database to eliminate joins is NOT a good idea.
My suggestion is:
If designing a OLTP system normalise as much as possible then denormalise to increase performance where needed. For A OLAP system look at star schemas etc and dont even bother with normalizing it first. Oh by the way most of the OLAP systems normally use a OLTP system as a data source.