And besides, this just aint us. It’s like being in a Halloween costume we can’t get out of.

Johnny responds,

Well, we got to get used to it…We’re in big trouble and it’s our looks or us.

This commenting goes on with Johnny proclaiming that he should not have brought a 13 year old kid into this. Think back in the novel when Pony lamented being treated poorly by Darry as the insignificant little brother. Also, consider how Pony described himself after he spoke with Cherry. He defined himself by his hair, by his innocence, and by his intelligence. After this incident though, Pony is questioning who he is and how his character is defined within this larger group. Likewise, Johnny’s identity is now questioned.

Johnny was the sweet kid, who wasn’t seen as very bright, or intellectual, but he is now understanding things that Pony wasn’t connecting and understanding. When these elements are considered together, they paint an uncertain picture about Johnny and Pony, but also about the group as whole. Does Pony actually understand who anyone is, becomes a third pertinent question. Since an overall theme of the novel is about identity, this seemingly inconsequential quote speaks highly to that theme. 

In my opinion, this quote sets Pony up to reconsider how he views life, the group, and what really binds them as a psuedo family. He is maturing and beginning to understand that his perspective about life may not be accurate. 

There is something about Ponyboy that sets him apart from the other Greasers. He is a good student who loves literature, movies, and sunsets. He has a sensitive, caring, and idealistic nature and has not yet become jaded like Dally or overwhelmed by the cares of the world like Darry. The other Greasers recognize and respect this and expect Ponyboy to act differently. Johnny calls this quality about Ponyboy "gold", and Two-Bit recognizes it also - when Ponyboy scares off a bunch of Socs with a broken bottle, Two-Bit is concerned that he might be becoming just another hardened Greaser, but then Ponyboy's real nature comes through, and he stoops in a very un-Greaserly manner to pick up the broken glass so no one will be hurt.

Ponyboy has always been better in school than Johnny, and he is surprised that Johnny can get so much out of a book.

After Johnny kills Bob, he and Ponyboy have to go on the run.  They hide out in an abandoned church waiting for Dally.  While they wait they kill time by reading Gone with the Wind.

Johnny sure did like that book, although he didn't know anything about [it], and I had to explain a lot of it to him.  It amazed me how Johnny could get more meaning out of some of the stuff in there than I could… (ch 5, p. 76)

Johnny is slow, but not stupid.  It takes him a long time to get a concept, but he likes to explore it to great depths once he has it.  He enjoys discussing the book and the concept of the “Southern gentleman” with Ponyboy.  Pony realizes that Johnny is very intelligent and sensitive when given time.

Growing up poor in an abusive household, Johnny never had much of a chance.  He is a sweet kid and has a good heart, and turns out to also have a good brain.  Pony finds it sad that Johnny has missed out on so much of his potential.

Pony is impressed to realize that there is more to Johnny than he thought.

When Pony and Johnny are on the run after the death of Bob the Soc, Pony gets to know Johnny better.  It has been clear that Pony is considered the brains of the greaser gang.  He gets good grades, likes to read books, and is generally a deep thinker.

Johnny brings Pony a book, Gone with the Wind, because he remembers that Pony once mentioned being interested in it.  Johnny thinks that he book will pass the time, and he actually is quite taken with it.

It amazed me how Johnny could get more meaning out of some of the stuff in there than I could--- I was supposed to be the deep one. Johnny had failed a year in school and never made good grades--- he couldn't grasp anything that was shoved at him too fast … (Ch. 5)

Johnny does not know much about the Civil War, the time period in which the book takes place, but he is very interested in the plot and finds deeper meaning in it than Pony thought he was capable of.  He realizes that even though Johnny never did well in school and his teachers thought he was dumb, he is actually quite bright.

When they notice a sunrise, Pony recites a Robert Frost poem that it reminds him of called “Nothing Gold Can Stay.”  Johnny likes the poem and comments that Pony seems to be unique in his family and in the gang.

"Well," I said, thinking this over, "you ain't like any of the gang.  I mean, I couldn't tell Two-Bit or Steve or even Darry about the sunrise and clouds and stuff. I couldn't even remember that poem around them. I mean, they just don't dig. Just you and Sodapop. And maybe Cherry Valance." (Ch. 5)

When Johnny is lying in the hospital about to die, he remembers the poem and tells Pony to stay gold.  This is a reference to the poem because he is telling Pony to stay innocent.  He wants him to get out of the gang life and take advantage of his intelligence to get an education.

Johnny is the perfect example of not judging a person based on looks.  He may seem like he is just a dropout gang member, but in fact he is a deep thinker.  Johnny and Ponyboy are both young men with more to them than meets the eye.

When you are trying to understand this line, you need to keep in mind what "deep" means.  In this case, the word refers to someone who thinks a lot, something like an intellectual, perhaps.  So Pony is saying that he thought he, rather than Johnny, is supposed to be the one who is always thinking about stuff.

Pony says this in reaction to the way Johnny gets into Gone With the Wind.  Pony is surprised at how much the book makes Johnny think and what Johnny gets out of the book.  Pony thinks he is supposed to be the thinker, and that is what the line that you quote means.