Conditional statements in 'manual' emails or thank you letters
Yes, what you are describing is the default setting for CiviCRM.

Only Message Templates and Automated Messages make use of the so called smarty template engine. The smarty template engines makes "if"-statements possible.
The reason for this is that these Templates and Automated Messages are for more experienced users and administrators. 

Normal mails, mailings and pdf reports can be used by regular CiviCRM users. And it might make their daily work much more difficult if they suddenly run into smarty template coding.

But, this is only the default setting.
In your civicrm.settings.php is an option to override this and expose the smarty template engine to normal email too:

/**
 * Enable this constant, if you want to send your email through the smarty
 * templating engine(allows you to do conditional and more complex logic)
 *
 */
define( 'CIVICRM_MAIL_SMARTY', 0 );


Set this to 1 and you can use "if"-statements in normal email.