I get trashed by
PRO_rANDY's amphbots when I'm cloak - maybe I'm not using enough ronin myself!
That said, to counter ronin the premium tool is Limpets in the early game and as
Aquanim mentions Grizzly. You can play an attrition game with the cloakbot user that their slings/phantoms don't solve, because they open themself up to easy amphbot countering via MORE limpets and duck.
If amphbots are broken, it's because they're a little too powerful right now - only slightly in the shadow of badgerspam. I played a number of hover vs amph games in recent times and came to the sad conclusion that hover have an extremely unfavourable escalation pathway against amph. Duck/Archer completely shuts down their raiding, Bouy their skirmisher and riots, and grizzly seals the deal. If they make lances, you can quite easily duckspam or lob your grizzly a single time. Limpets trivialize bolas too.
The bulkhead nerf was good, I think scallop deserves to become relevant again but bouy might need to be toned back down.