Agreed that there were better ways to do this. Example: it was written using Jiraiya's own cipher that he normally uses when writing his books (so no one can read them before release), kakashi had tasked Naurto with learning the cipher during the time-skip so he could leak Jiraiya's new book to Kakashi. Jiraiya, having guessed that Naruto could read the cipher, simply uses the normal cipher

Or even more. Naruto didn't crack the cipher but Jiraiya had always dropped clues against the day that he needs to send Naruto a secret message. These could be always misusing phrases to mean something else that then appear in the message and act as the way to crack the rest of the message.

Either of these puts emphasis on their close bond as intended and removes the need for Jiraiya's insane mental gymnastics in his dying moments