When the stored procedure is processed by the server it is parsed and then 'unparsed' into a format that is more 'correct' to the server. This removes most formatting and explains what you are seeing.
This typically isn't an issue because many (most?) development teams store their SQL as script files in their source control system and edit from there as opposed to from editing from the database definitions directly.
One final note. If you use Sybase Central to edit your stored procedures, it will preserve the formatting of the procedures for you.
--Jason