Seymour Hersh never said that.
The article you linked appeared on May 19, 2009. Later that same day, dawn.com published a retraction, saying that they "regret the error".
The retraction includes the following statement from Hersh:
Vice President Cheney does not have a death squad. I have no idea who killed Mr Hariri or Ms Bhutto. I have never said that I did have such information. I most certainly did not say any thing remotely to that effect during an interview with an Arab media outlet
[...]
I have never been asked by any journalist...about such allegations. This is another example of blogs going bonkers with misleading and fabricated stories and professional journalists repeating such rumours without doing their job -- and that is to verify such rumours.
(His use of the phrase "does not have a death squad" is interesting: by 2009, Cheney was out of office and so nobody would have expected him to be currently controlling a "death squad" or any other military or paramilitary unit. You'd think Hersh would have said that Cheney did not have a death squad, but he didn't say that.)
I suppose an extremely skeptical person could consider the possibility that Hersh had made the claim and was trying to backtrack it. However, the original article cited the claim as having come from a May 12 interview that Hersh supposedly gave to Gulf News. Had the interview actually existed and contained the claim, it should have been easy for dawn.com to find it, and they would have an incentive to do so in defense of their original story.
Hersh did say, in a speech at the University of Minnesota on March 10, 2009, that Cheney oversaw an organization called the Joint Special Operations Command, which Hersh described as an "executive assassination wing". As quoted in an opinion piece by Eric Black on MinnPost, March 11, 2009:
Right now, today, there was a story in the New York Times that if you read it carefully mentioned something known as the Joint Special Operations Command — JSOC it’s called. It is a special wing of our special operations community that is set up independently. They do not report to anybody, except in the Bush-Cheney days, they reported directly to the Cheney office. They did not report to the chairman of the joint chiefs of staff or to Mr. [Robert] Gates, the secretary of defense. They reported directly to him. …
“Congress has no oversight of it. It’s an executive assassination ring [sic, see below] essentially, and it’s been going on and on and on. Just today in the Times there was a story that its leaders, a three star admiral named [William H.] McRaven, ordered a stop to it because there were so many collateral deaths.
“Under President Bush’s authority, they’ve been going into countries, not talking to the ambassador or the CIA station chief, and finding people on a list and executing them and leaving. That’s been going on, in the name of all of us.
He does not appear to have given any more specifics, and did not mention Benazir Bhutto or anything about Pakistan specifically. The phrase "death squad" does not appear.
The MinnPost piece has a link to an audio recording of the speech which unfortunately is broken, and I haven't found it elsewhere.
In an interview with Democracy Now on March 31, 2009, Hersh was asked for more details. He claimed that the group was operating in "at least a dozen countries and perhaps more" but refused to be more specific because he "hadn't written about it". He did give as possible examples ("let's say") Yemen, Peru, Colombia, Eritrea, Madagascar and Kenya, but did not assert outright that assassinations had taken place in those countries. He never named Pakistan.
Regarding Cheney's involvement, he said:
And where Cheney comes in and the idea of an assassination ring — I actually said “wing,” but of an assassination wing — that reports to Cheney was simply that they clear lists through the Vice President’s office. He’s not sitting around picking targets. They clear the lists. And he’s certainly deeply involved, less and less as time went on, of course, but in the beginning very closely involved.
I haven't found any indication that he ever published a fuller account of these claims, nor any evidence for them.
For the New York Times article referenced by Hersh in the March 10 speech, Black gives a link to "U.S. Halted Some Raids in Afghanistan" (March 9, 2009). The article says that US Special Operations raids in Afghanistan were suspended for two weeks in February 2009 over concerns about civilian casualties. It makes no mention of any operations during the Bush/Cheney administration, nor does it say anything about operations taking place anywhere else outside Afghanistan.
Note I have not addressed the question of whether Cheney actually did order Bhutto's assassination, because it turns out that no notable source has made that claim. Dawn did not claim that he did; they only claimed (incorrectly) that Hersh had claimed it. And Hersh in fact didn't claim it either. So unless another source is found, that particular question is off topic.
As to Avery's comment below about the "death squads" being "confirmed" by the New York Times, this seems to refer to "Cheney is Linked to Concealment of C.I.A. Project" (July 11, 2009). That article only claims that some secret counterterrorism program, not further identified in the article, was not disclosed to Congress on Cheney's orders. It says that the program, whatever it was, "never became fully operational" and only involved planning and training. The New York Times did not, by any stretch of interpretation, "confirm" that Cheney had a "death squad".
