In the graveyard scene, Mr. Brooks tells Mr. Smith (Balford) that the content of his safety deposit box has vanished. How did he get rid of that content to make sure no one knows about the pictures after Balford's murder?
The film is rather vague around this point, but there are a couple of clues. At one point we hear this exchange (source IMDb):
Mr. Brooks: Where do you think he has the other pictures?
Marshall: He put them in a safety deposit box. But I'll bet the box is at the bank where he keeps his checking account. The key... is on his key chain! He really wants to do this. He's not going to the cops.
This establishes that Mr. Brooks knows where Mr. Smith is hiding the photographs.
Later, there's a scene where Mr. Brooks breaks into Mr. Smith's apartment. According to the screenplay (PDF), we witness Mr. Brooks make a wax impression of that safety deposit box key.
A keyring. Hands in surgical gloves isolate the - safety deposit key - and press it into a soft wax block where it leaves its impression. The light goes off.
So we're supposed to assume that Mr. Brooks just made a copy of the key and went down to the bank and removed the incriminating photos. That's not really how safety deposit boxes work, though. They're not like lockers at the gym. The bank won't let you into one just because you produce a key. I guess the producers of Mr. Brooks were counting on most people not knowing this (or they didn't know it themselves), which is actually not that surprising, considering one article I found that says that only 6% of bank customers rent a safe deposit box.