There is some caveat about Drupal coding conventions, here's an exhaustive list of coding convention we bypass:

String concatenation
The fact is Drupal 6 coding convention asks for:
$str = 'static'. $dynamic .'static'
We always do string concatenation like this:
$str = 'static' . $dynamic . 'static'
Which is the way of Drupal 7.
CamelCase in classes
Drupal would do:
    class some_class {
      public function hello_world() { }
      // See here name collision
      protected function _hello_world() { }
      private function _hello_world() { }
    }
Zend would do:
    class SomeClass {
      public function helloWorld() { }
      // Name collision avoided
      protected function _helloWorld() { }
      private function __helloWorld() { }
    }
Which is we always do. Only for real OOP code. We still keep the 2 spaces indent size.
PHPdoc
Drupal tells you to do:
    /**
     * My function does this, and it's pretty cool!
     *
     * @param $lolz
     *   Mixed array of stuff that makes my lol catz!
     * @param $catz
     *   The catz cited above
     * @param $killall = FALSE
     *   (optional) Should I kill the kitten
     * @return
     *   Some value you probably already hate
     */
Zend would tell you to do:
    /**
     * My function does this, and it's pretty cool!
     *
     * @param array $lolz
     *   Mixed array of stuff that makes my lol catz!
     * @param LolCatz $catz
     *   The catz cited above
     * @param boolean $killall = FALSE
     *   (optional) Should I kill the kitten
     * @return SomeType
     *   Some value you probably already hate
     */
Which is somewhere more likely because some IDEs will use this information to do better code completion and code folding.
This won't hurt your Doxygen.
LIMIT in SQL queries
You will see a lot of
SELECT 1 FROM {some_table} WHERE [some conditions] LIMIT 1
Drupal would tell you to use db_query_range(), but in our case, there is no need for this. The SELECT 1 (or often TRUE is a way to determine if an object exists in database. The LIMIT 1 is a a performance fix to ensure our DBMS won't fetch useless results.

You don't like it, this is none of our business. Those standards are here for proper code readability. Zend coding standards are only used for PHPdoc (full module wide), and OOP parts.