Did Keller get found in the end?

It cannot be determined, but the chances of Keller being found by Loki is high based on Loki's expression after listening to the faint whistle sound twice and also we were shown in the movie that Detective Loki is good with details and connecting dots.

In an interview with screenwriter Aaron Guzikowski it is explained that an ending where Keller is found by Loki was actually filmed, but was deliberately decided against in favour of a more ambiguous ending:

On the decision to end the movie with a cliffhanger:

“Oddly enough, that’s how it was in the script when it was bought. And it never really changed. When we were shooting, we did shoot a version where it goes a little beyond where the fade out is. There’s a version where he moves the car and sees Hugh down there, and so on. None of us really wanted to do that version, but we wanted to make sure we had it in case once the film was put together it seemed like it really needed it. But after testing the film with the ending it has now, everyone decided that was definitely the way to go. Joel Cox, the editor, felt very strongly about it. I just think that’s the moment when the movie is ready to end.”

And the ending that was shot but didn’t get used was…

“They move the car. They see he’s down there. You know he’s going to be taken out of the hole. I like it much better being ambiguous. Even though you assume that’s what’s probably going to happen, I like that there’s a small chance that he’s not going to get him out of there for whatever reason.”

But Detective Loki is so tenacious during the movie. Is there a scenario where he’d actually walk away?

“No, I think there’s a small percent chance that for some strange reason he might decide not to get the guy up. In my mind he would: Those two guys have a strange connection that they form over the course of the movie. That seems to be the logical next step for Jake’s character at that moment.”

On why the studio was (atypically) fine with an oblique ending: “

I was very surprised that we were allowed to keep that ending. I was surprised I was able to get the movie made, actually. It’s a pretty dark script. Especially ending the way it does. It’s definitely a testament to Alcon, the producers on the movie, sticking by the script and not wanting to make it into something it wasn’t.”

In a fantasy world where we saw what happened to Keller after he’s out of the hole, things would not have gone well for him:

“I think, unfortunately, he would go to prison. The final irony — his father was a prison guard, and the whole movie is metaphors of people’s internal prisons, external prisons. I believe that’s what would end up happening to him: that he would go to prison for some time.”

I've just watched the movie and then came here to look for questions asked about it. My interpretation of this particular scene is as follows:

It was very clear to me when I saw it. Loki will find Keller and of course rescue him. Everything was set for it even from earlier in the movie when Loki came to Mrs. Jones' house for the first time and inspected the Trans-Am outside, when he found out about the whistle in the hospital, when the CSI people shut down the humming of their machinery and shut off their music player. Even his final reaction of shrugging his shoulders with disbelief before hearing the dim sound of the whistle for a last time was a clear sign of what was going to happen next.

All of these together did set off the scene for Loki to realize what was going on. There wasn't any meaning to show the actual rescue because we already got the message and it would spoil the message to a degree. All of the protagonists and antagonists are in one way or another 'prisoners'.

The faint whistling was actually supposed to make it harder to decide either way. The movie ending without it would have suggested they never found him.

I mean it the movie way, not the common sense way. Otherwise I agree with chaitanya89 (see the first answer). There is some chance for him to be found. Loki is a tenacious detective indeed. However, I think that answers another question: "Are there reasons to hope they found him?".

The ending is intentionally left ambiguous, fitting a morally ambiguous character.

The ending was purposely left ambiguous. There was an original ending where Loki moves the car and finds Keller but the filmmakers changed it on purpose and the studio ultimately left it as is. The ending does show that Loki hears the whistle, but we don't see him actually find Keller. So it may be that he decides it was just the wind, or it may be that he finds him but decides to leave him to his fate, or it may be that he finds and rescues him. I think the most likely conclusion given what we know about Loki is that after hearing the whistle, he investigates the area more until he finds Keller and rescues him from the hole and then Keller goes to prison for what he did to Alex.

Here are some comments from a buzzfeed article interviewing the screenwriter and addressing these questions.

Did the whistle work, for God's sake? ... I talked to Prisoners screenwriter Aaron Guzikowski about the ending.

On the decision to end the movie with a cliffhanger:

"Oddly enough, that's how it was in the script when it was bought. And it never really changed. When we were shooting, we did shoot a version where it goes a little beyond where the fade out is. There's a version where he moves the car and sees Hugh down there, and so on. None of us really wanted to do that version, but we wanted to make sure we had it in case once the film was put together it seemed like it really needed it. But after testing the film with the ending it has now, everyone decided that was definitely the way to go. Joel Cox, the editor, felt very strongly about it. I just think that's the moment when the movie is ready to end."

And the ending that was shot but didn't get used was...

"They move the car. They see he's down there. You know he's going to be taken out of the hole. I like it much better being ambiguous. Even though you assume that's what's probably going to happen, I like that there's a small chance that he's not going to get him out of there for whatever reason."

*But Detective Loki is so tenacious during the movie. Is there a scenario where he'd actually walk away?

"No, I think there's a small percent chance that for some strange reason he might decide not to get the guy up. In my mind he would: Those two guys have a strange connection that they form over the course of the movie. That seems to be the logical next step for Jake's character at that moment."*

On why the studio was (atypically) fine with an oblique ending:

"I was very surprised that we were allowed to keep that ending. I was surprised I was able to get the movie made, actually. It's a pretty dark script. Especially ending the way it does. It's definitely a testament to Alcon, the producers on the movie, sticking by the script and not wanting to make it into something it wasn't."

In a fantasy world where we saw what happened to Keller after he's out of the hole, things would not have gone well for him:

"I think, unfortunately, he would go to prison. The final irony — his father was a prison guard, and the whole movie is metaphors of people's internal prisons, external prisons. I believe that's what would end up happening to him: that he would go to prison for some time."