I've always had problems doing so;  they spawn early game, when Vodyani have little to no presence aside from their second ark, which doesn't help as a single ark isn't enough to win the ground battle, especially if you're lacking in manpower, as vodyani often are.

What i do with them is; don't play as vanilla Vodyani. Custom it, and take that Gaugantua pop trait out so you don't get -50% food system penalty. You get more manpower that way, and your pop can grow by food without need to rely on essence.

In my last game I spawned without any tutanium nearby  -- so no siege module, and thus I was unable to clear a (hard) pirate nest despite almost constantly camping it until turn 62! It simply upgraded faster than I could produce manpower.

The Vodyani still feel very weak in general, but being completely unable to wage ground battles until you have researched siege modules, or several food and manpower techs seems to be one of their most glaring issues. Some ability to convert industry to manpower, like for the riftborn, would be most welcome.

If you got multiple pirate lairs on your coast its gonna be difficult I agree.

the rest depends on the build order, one tactic you can use is border pods on low class ships. you need the enhanced shielding research and the boarding pod research than you go eco. border pods are a perfect counter depending on the planets you inhabit.

try this tactic. Also after some research you can level up arks.

Hero and first explorer fitted properly deal with them easily. Once initial ships are beyond rookie they take them out no problem. Then either fit a leecher with siege mods, or use manpower to reduce population

to take out quest pirates you can use exploration ships or ark that is not outfitted with missiles. Pirate lairs can be killed off by a fleet with siege modules, if you don't have titanium you can rush marketplace and buy it there