I'm having similar problems with one of the Pirate Hunting Missions. You need to kill a SPECIFIC Pirate faction. Not just any wanted pirate will do. But the problem is... There is like a handful of these guys in the system!
I did one last night where I had to take out 24 pirates, and it took me literally 5 hours to get that many! I made the mistake of accepting several of these at once, and now today, I am on another one that required 16 from a specific faction. After checking res sites, USS, Nav Beacon and just flying around aimlessly in SC, I have managed to kill 6 in the last 3 hours!
I think the problem here is that FD has not bothered to check the game mechanics to see how many of the required target the game is generating! Just like your Skimmer mission, these pirate missions just don't have the required number of targets! I'm definitely not taking any more of these missions, and the same goes for that Skimmer mission you posted about!
From an immersion stand point... Seems highly unlikely that a group of pirates so small would warrant a mission with 2.5 million CR reward! lol!
Stupid Grind once again! Just plain stupid.