Ferroseed seems like the perfect Kingdra counter, until you realise that its basically setup bait for 99% of the metagame. Running a set of Spikes/Leech Seed(these 2 are virtually mandatory for Ferroseed) means that you only have 2 slots to maneuver around. Things like TWave/Toxic/Protect are great for seed, but one of the best reasons why Ferrothorn is good in ou is the ability to threaten bulky waters through power whip, which Seed lacks.
Another thing is that Ferroseed's attack is a pathetic 50. it's basically as low as togekiss and azumarill, except seed doesn't have an ability that raises attack. Bullet Seed does pittance on Kingdra: if you are investing in max defenses, here's what happens:
5-hit 4 atk bullet seed vs 180/0 Kingdra(chestoresto): 23.7 - 31.2 %
this is shit, when you're seeing that its 5 hits. remotely threatening? fucking shit, its not. unless you use leech seed, in which case its impossible to stall forever because ferroseed is slow as fuck. ferroseed can't stall kingdra out easily unless somehow tspikes is on and kingdra user doesn't have a way to remove tspikes
kingdra is great and all but no, ferroseed is a crap counter at the end of the day. it just sits there... and annoys the fuck out of kingdra. unless its a last-poke situation, kingdra basically wins by swapping to chandelure and spamming random overheats.