In the Drupal community, we always recommend using the Drupal API, and best practices for development, management and deployment. This is for many reasons, including modularity, security and maintainability.
But it is also for performance that you need to stick to these guidelines, refined for many years by so many in the community.
By serving many clients over many years and specifically doing Drupal Performance Assessments, we have seen many cases where these guidelines are not followed, causing site slowdowns and outages.
Here are some examples of how not to do things.
Logic in the theme layer
We often find developers who are proficient in PHP, but new to Drupal misuse its API in many ways.
In extreme cases, they don't know they should write modules to house the application logic and doing data access, and leave only presentation to be done in the theme layer.
We saw a large site where all the application logic was in the theme layer, often in .tpl.php files. The logic even ended with an exit() statement!
This caused Drupal page caching mechanism to be bypassed, resulting in all page accesses from crawlers and anonymous users to be very heavy on the servers, and complicating the infrastructure by over-engineering it to compensate for such a development mistake.
Using PHP in content (nodes, blocks and views)
Another common approach that most developers start using as soon as they discover it, is placing PHP code inside nodes, blocks or views.
Although this is a quick and dirty approach, the initial time savings cause lots of grief down the road through the life cycle of the site. We wrote an article specifically about that, which you will find a link to below.
Heavy queries in the theme layer, when rendering views
In some cases, the logic for rendering individual nodes within a view is complex, and involves code in the view*.tpl.php file that has SQL queries, or calls to heavy functions, such as node_load() and user_load().
We wrote an article on this which you can find the link to below.
Following Drupal's best practices and community guidelines is always beneficial. Performance is just one of the benefits that you gain by following them.