The thing with his father is just a personality quirk of his. Just something to make the character more interesting (though after 5 seasons now it's definitely something useless to the character and his development). It's the equivalent of an imaginary friend.
*************Some small spoilers beyond this point**************
Something else kind of interesting in regards to it. Through the first few episodes I really thought Edward James Almos' character was a figment of Hank's imagination the same way dexter sees his dad. Through the first few seasons the big killers that Dexter tracks through the season always had some trait that Dexter could relate to, or some kind of connection and I thought that this would be it for this season. Up until the episode before last they really made it seem that way, and even in that episode there is a scene of hanks and almos in the cafe where the one chick asks hanks if he wants more and completely ignores Almos sitting right across from him entirely. But they then later show that Almos ties her up.
I don't know, there is something really wierd going on with Almos and the way he is portrayed in relation to Travis(hanks) and the rest of the world (besides of course that he's a homicidal maniac to normal people and someone who talks to god to Hanks =P). Even in the scene where the girl is tied up she never even acknowledges Almos standing right over her, she is purely concentrating on Travis. And the one professor that batista and the other guy go to visit has that box of stuff of his that's got his name written on it like it's an evidence box or his last personal effects (and they not so subtly hint that she's much more involved than the detectives want to think, even after they find the notebook, it's pretty obvious she's playing them).
Do have a theory or two about it =P
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?It's a sad thing not to have friends, but it is even sadder not to have enemies.? - El Che