Is it possible, that shakturi posess an extremely strong ECM making them invulneable to gravitics? Ion defense maybe? Would be good to know for my own designs.
As far as I am aware, the only special toys that the Shakturi possess are Shaktur FireStorm torpedoes and the superweapons. No special ECM components, no special targeting components, no special ion defense components.
Beyond that, ECM does not directly protect a ship from gravitic weapons. It makes the ship harder to hit. You were able to take out the shields of your target with your blasters, and so presumably you were able to hit your target with your weapons. Ergo, the target did not have some sort of superb ECM system. Ion Defense, to the best of my knowledge, is completely useless as a defense against anything that isn't an Ion Cannon or Ion Pulse (or a modded weapon with the same damage type), aside from the whole "RNG says the last blaster shot hit the Ion Defense rather than the Fighter Bay" aspect.
And as the manuells say that gravitics bypass both shields and armor, I expect 100 ships of size 600 and a gravitic firepower of 600 each to do so and crack a single shakturi frigate!
It appears to be true that gravitics bypass both shields and armor. However, this does not make gravitics good primary weapons. Gravitics tend to be short-range weapons, the tech description implies that their performance scales in some way with the relative size of the ships engaged, the weapons suffer range penalties, and the weapons offer poor DPS density. The Maxos Blaster I (the component as it is when none of the improvements for it have been developed) offers a DPS density of 0.81 DPS per size unit at 0 range. The Graviton Beam I, by comparison, offers only 0.11 DPS per size unit. Even the Seeker Missile, the primary weapon with the lowest DPS density available, more than doubles that, with a DPS density of 0.23 DPS per size unit.
Graviton Beams and Resonant Graviton Beams are much better as secondary or specialty weapons, much like Ion Cannons and Tractor Beams. Much like Ion Cannons, they degrade the performance of an enemy ship while the primary weapons beat it down and kill it the old-fashioned way (by destroying components, unlike Ion Cannons which merely disable components). Much like Tractor Beams, Graviton Beams and Resonant Graviton Beams hold the target in place while your other weapons deliver the beating, and unlike Tractor Beams the Gravitons do a little damage on the side (of course, they also don't pull the target in closer or push it away, if my memory is correct, whereas Tractor Beams do). What Graviton Beams and Resonant Graviton Beams do not do is provide a significant amount of offensive power. The firepower statistic that the game provides is the sum of the weapon damages for every weapon mounted on the ship, which is an approximation of the ship's alpha strike damage or its damage per firing cycle, but this does not consider (and in many ways conceals) the effect of the firing interval - two size-10 weapons which each deal 10 damage per shot both increase a ship's firepower by 10 per weapon mounted, but if one of them fires at twice the rate the other fires, do you think that a ship which mounts the slow-firing version is any real match for a ship that mounts the fast-firing version if the ships are otherwise identical and the slow-firing weapon has no advantages in terms of attack range or energy-efficiency? Your primarily-Graviton Beam ships have to get well into blaster range to engage the Shakturi's blaster-heavy ships, and even low-end blasters like the Maxos I have significantly better DPS. Your Gravitons probably deal some damage, but even though they're bypassing shields and armor they're probably not going to survive long against something with up to 30 times the DPS (Titan III versus Graviton I at 0 range, not terribly likely but possible; Titan IIIs additionally have roughly 4 times the range and don't have quite as much of a range penalty relative to the base shot power, so there could be ranges in which both weapons can fire where the relative difference in power is even worse) or kill it without some other significant advantage.