In my short work experience I found self-taught developers to perform better than formally educated ones.
The reason I gave myself for this is that a very relevant part of our job is spent in finding, reading and understanding documentation (and when documentation is not there, to find a solution anyway or die trying). As a self-taught developer, you will have spent years looking for and interpreting learning resources, while educated ones may have been spoon-feed.
Even worse, a student may (read "will") fall in the trap of only learning the strictly required material needed to pass the course and will rarely expand its knowledge using the force of the curiosity, which is what moves a self-taught developer in the first place.
Getting back to difficulties:
Being a self-taught developer is still great.