Their main flaw is that stack as many MRP's as you like, a couple well placed seeker salvos once the shields are down and it's bye bye hardpoints.
Seekers and hounds are OP vs hull tanks IMO and I dont even bother anymore. Also its a press to win weapon so not big deal if I loose against it.
Seeker, or any weapon with 'splash damage' do pose a threat. But there are options. ECM, PDT, and positioning. MRP's do resist splash damage especially if you have more than one MRP. Their damage absorption is multiplicative, and have DR, but two to three decent sized MRP's can keep you in the fight. I often fight with malfunctioning weapons. I apply Hull points to the, well hull, and an HRP or so, to give some bulk, but I do focus more on MRP's for my play style.
There are no counter against hounds, and it seems unfair to force an ECM or PDT to sacrifice an important utility slot specially as the FAS has only 4.