Stone reportedly asked his lawyers to try for a second pardon from Trump because Stone was worried about being convicted in connection with January 6.
Assuming the reports are accurate, and assuming the request for a pardon made it to Trump, it's unclear why Trump didn't grant it (Trump is obviously not one to worry about appearances, no matter how slimy they may be). My first thought was that Trump (upon advice from lawyers) wanted Stone to be able to take the 5th and refuse to answer questions to protect Trump. However, prosecutors could grant Stone immunity and force him to cooperate under threat of contempt so that seems like it's probably not the reason (I'll concede that this is highly speculative on my part).
On the other hand, Stone did take the 5th in a deposition by the January 6 committee:
>>>Roger Stone, a staunch ally of former President Donald Trump, met briefly Friday with the House select committee investigating the January 6 riot
and asserted his Fifth Amendment rights to every question asked, he said.<<<
As Trump has said, taking the 5th implies guilt:
>>>“So there are five people taking the Fifth Amendment, like you see on the mob, right? You see the mob takes the Fifth. If you’re innocent, why are you taking the Fifth Amendment?” . . . “When you have your staff taking the Fifth Amendment, taking the Fifth, so they’re not prosecuted, when you have the man that set up the illegal server taking the Fifth, I think it’s disgraceful,” <<<
Over the years, the former president has generally criticized other politicians for taking the Fifth Amendment. But on Wednesday, he invoked the right himself.
If you think I'm saying Trump has a double standard, you would be correct.