Hummm just to put things into perspective for players that never met hunter-killers, a while ago a played a big challenge game, and hunter-killers started spawning when i was holding something like 30-35 planets. A single mk3 HK was enough to destroy my entire fleet of fleet ships and starships in a straight confrontation and come out with some health remaining. If i added my fleet of golems to the mix i'd win and have some survivors, but if i got more than 1 mk3 HK or a single mk5 HK, one of my chokepoints (filled with all the trader goodies + lots of turrets and fortresses) + my entire fleet of ships + all my starships + my golems would almost certainly lose in a straight fight. The only way to tip things in my favor was to use a pile of tricks like using a fleet of transports to eat the first volley so my ships would shoot at least 1 bullet and using stealth to guarantee my bombers 1 shot and hopefully 2-3 shots before disappearing.
Still, only 1 thing ever managed to let me win against multiple HK or a single mk5 HK, and that was to use my golems to lure the couple 1000 of ships that were travelling with the HK away from the wormhole to my inner systems, let the HK destroy my base, jump my golems out for a second so the HK would take the wormhole to my inner systems but get my golems to come back before the fleet ships followed them and left my chokepoint.
After that i would speed rebuild my chokepoint to take care of whatever (huge) number of ships would remain there, and in my inner systems i used a weakness of the ai to take down the HKs over a period of 20-30 minutes. It seems they liked to run after my leech starships more than my bombards, so i'd have my leeches running circles around them in a corner of a map while my bombards were slooooowwlly taking them out. Yep, their only exploitable weaknesses i could find were their relatively low range and the fact that bombards were not high enough on their kill list, otherwise i could find no way to stop a single mk5 hunter killer (even with the research and economy of a 30+ planet empire) or a couple lower marks.
The big issues were that there were no spire ships back then to help take them out, being on my own planet didn't give a speed boost, trader toys had too little effect to make a difference, and also as someone else said, they kept their entire firepower until the very end, contrarily to say the avengers. Avengers were wimps compared to hunter killers.
Have fun!