Has there ever been a Holy Grail War where the victor got their wish?
Yes, one: the only Holy Grail War in the world of Fate/Grand Order, whose victor was the founder of Chaldea and its first director Marisbilly Animusphere with his Caster Servant,


   Solomon.


As for what he wished for, it's not clear but Servant Sherlock Holmes (yes really) speculates in the Camelot chapter of the game that it was a wish for Chaldea, the work of his life, to succeed:


  Sanzang:
  
  Umm… Can I ask something?  I’m not trying to complain that I’m tired
  of keeping quiet all this time, but… You said that Marisbilly guy got
  the Holy Grail, right?  What did he wish for?
  
  Holmes:
  
  Unfortunately, Hermes has no record of his wish. It only shows the
  results.  According to Hermes, Marisbilly flourished as a magus after
  the war.  In the Clock Tower, Chaldea and the Animusphere family’s
  theories had heretofore been regarded as abstract and impractical. 
  But, a string of successes reversed the Animusphere’s fortunes. The
  Heroic Spirit summoning system was established.  Virtual experiments
  were conducted that allowed one to not only observe the future, but to
  interact with different time periods through rei-shifting.  Around
  2004, Chaldea, previously a mere astronomical observatory, was built
  into a research facility.
  
  Conventional reasoning would conclude that Marisbilly wished for
  prosperity.  He had no reason to wish for the incineration of the
  human order. According to documents, his personality was
  “hard-working.” He had ordinary desires, ordinary envy, and he loved
  ordinary fortune. That’s the kind of man he was.