Pirates are the faction I'm least interested in and the one I have the least experience with. In fact, I've played only a single game with them and didn't even finish it. The Crossfire expansion for original SMAC was criticized for introducing factions that didn't have a strong ideological base (unlike the base factions). But, enough of that. I can still lay out a strategy for them and it's fairly straight-forward with the Pirates.
The single biggest advantage Svensgaard gets is the terrain modifiers: Extra food on Ocean and extra energy on Shelf. You say that the sea isn't very productive - that's true for standard factions, but Svensgaards bonuses are meant to remedy that. Svensgaard is basically the only one who can build viable bases in the deep sea, thanks to these bonuses. This means that what is by far the single largest area of the map on most map types - the open sea - is virtually uncontested. Everybody else will be fighting for every inch of land while you own ~70% of the map by default, and nobody will have much interest in nor capacity to challenge you there. Other than having to fend off those Isles of the Deep as you mention (which can indeed be a problem) this means you have incredible offensive power since you can have just a token defense and commit almost all units to attacking/raiding...
.. which leads us to the piracy. Svensgaard is similar to Yang and Santiago in that he is focused on military production, specifically naval units - and Boat class units in particular. All of your naval units have what is essentially an improved version of the Scavenger promotion: They get both the Scavenger promotion itself, and they additionally steal research by pillaging [against more advanced opponents]. Thus, pillaging tiles is very strong with the Pirates. The strategy, then, is to play them exactly like you would expect from a pirate: You want to become the terror of the seas, relentlessly pillaging and plundering those landlubbers whenever they so much as think about putting bases in or even near the ocean. You'll have to decide beforehand who's going to be allies and who will be enemies, though, because you probably want at least some stable trade route income and unless you want to be at war with the whole world at once you'll need the Irregular[/i] promotion on most of your Boat units. This is why the Svensgaard AI is so reluctant to open borders: The Irregular promotion prevents raiding open border signatories, raiding being a vital Pirate strategy. The piracy is essentially how the Pirates keep up in the tech race: Zakharov develops the tech, Roze steals it, Svensgaard pillages for it. Svensgaard essentially turns minerals into research in this way, building lots of Boats which then go and create free research for you by pillaging, slowing down your opponents in the process. It's specifically the top half of the tech tree you want to raid for - your own research should be focused on the bottom half of the tech tree, which is where all the juicy sea-related stuff a pirate needs is found. If your navy is sufficiently more powerful than everybody else's and they have many coastal improvements you may never want to sign any open border agreements at all so that you have hands untied to plunder every single sea tile improvement the other factions ever build. Be careful not to overdo it, though: You actually want them to keep expanding into the sea, so you can keep plundering them for tech! Once you reach the Biofuel tech and can adopt the Autarky civic (which prevents foreign trade routes anyway) this option becomes even more attractive, especially as Autarky is where you'll likely want to go as you hopefully have many bases scattered all over the best areas of the sea at this point.
In fact, let's round this off with a civics review. The default civics Svensgaard is aiming for will almost certainly be Police State/Autarky/Power/Biodomed/Non-member. Police State can possibly be replaced with Fundamentalist - especially if you managed to found a religion, which will probably be ascetic virtues - but you'll almost certainly want a massive navy at all times, and Police State will get you that. It will also help produce the Sea Colony Pods you will want to plaster the entire map with. Democratic isn't that attractive for Svensgaard since it only works well with large amounts food and infrastructure, neither of which you are likely to have (your only key infrastructure is the Naval Yard). It seems pretty strange to me being one of the select few to have escaped an irradiated Earth only to build up an authoritarian regime based on piracy, but I digress... Ahem. Back to topic. Both Autarky, Power and Non-member are almost set in stone for the Pirates: You aren't going to be opening borders much, which devaluates Free Market, and outside of the early game your capital probably won't be hugely larger or better than other cities and sea resources may not be giving you a large food surplus, ruling out planned. Autarky takes a while to unlock, though, but you are looking at a situation typically similar to Deirdre with many small bases so it's no surprise you'll want 'her' civic. Power sits at the upper part of the tech tree, outside of your focus, but there's really no reason to run anything else once you have it: You want to steal/pillage for techs rather than research yourself, ruling out Knowledge (whereas Power as great for these things), and you'll be building lots of Boats and Sea Colony Pods so Wealth is terrible. You aren't interested in Council membership since you don't have [much] foreign trade and being able to pillage is vital. The only thing really up for grabs is your approach to Ecology - all options are situationally viable, but Biodomed is your go-to option for the energy bonus for your kelps and, later on, the free Stealth promotion for your enormous navy.
