Whilst you aren't exactly wrong, the relative blind spot present in Shiplord doctrine pre-Sphereic War isn't without precedent. Human polities are notorious for creating the weapons with which to fight the last war, and for pretty much all of Shiplord history up until their encounter with the Sphere, War Fleets in combination with certain…special assets had always been enough.
It is indeed the case that the War Fleets of the Shiplord navy were and remained significantly more deadly than their Hjivin counterparts, but that meant relatively little when the Sphere's mechanism for taking planetary systems involved a total focus on what was inside of the Stellar Exclusion Zone.
The vast majority of lifebearing worlds exist in that zone, and the Sphere's active invasion tactics were brutally utilitarian. Deploy enough Regular Fleet type craft (that the Shiplords largely lacked at the beginning of the war) to simply ignore the winnowing effect of War Fleet fire.
Once beyond the range of the War Fleets, they could dismantle the inner system at their leisure.
Did they take significant casualties from every assault? Yes. Did they care, and did it matter? No, not particularly.
The problem here is multi-facted, and not at all as simple as it appears. The Shiplords had never encountered a polity capable of warfare as the Sphere executed it with an industrial base sufficient to do so against them (the Shiplords). Oh, it could be done with drone fleets or AI-manned craft but they were old hands at turning those sort of forces against themselves.
Doing so with manned craft? At the sort of scale required to succeed? It sounded insane - what sort of polity would just throw away millions of lives like that? Answer: the Sphere.
But it's also…not the actual problem. Or at most only one part of it. The way in which Contact was trained could've allowed for a more aggressively investigative approach to the Sphere, one that might have forced them to realise that the Shiplords truly were as old and powerful as they said. This wasn't a matter of guns ready on the border, it was about perception and ideology.
Would write more but have to drive 8-10 hours now. Please be kind to any errors I might've made rushing this.
Er, human polities being prepared to fight the last war is fine and dandy when you're talking about 20th century human polities who measure their history in centuries with populations and leaders who don't live to see a century at best, with technology, resources, political will, and industry that is quite limited and needs to be rationed across a plethora of serious societal needs where the stakes are life and death.
Shiplord society, even in the centuries leading up to the encounter with the Sphere, was ancient, possessing of insane technology and resources across the board, the skill and industry to ramp up and apply those to build a massive war reserve and rapid-mobilization regime in the event of a full-on galactic war breaking out without warning, combined with the population and political will to push such a measure through with confidence.
Given that Shiplord society was all about discovering, countering, and preventing abuse of Secrets (ESPECIALLY on a massive scale), preparing for such a scenario on a galactic scale with no warning should have been a fairly obvious course of action. Even if they didn't know exactly what kind of military might they would most need, they DID know that they could stockpile a massive amount of military might of various kinds to at least be effective (even if not ideal) in any scenario they could imagine. As an example, the scenario in which the enemy employs vast numbers of cheap combatants across an enormous front is not only easy to imagine, it is easy to envision as a likely enemy tactic for the simple purpose of distraction. War Fleets are extremely powerful, but if you only have a small number of them, then it seems obvious that the easiest counter to such an asset would be to have cheap threats present everywhere at once. The Regular Fleets was the counter that was developed for this, but the fact that such a counter had to be developed after the fact says everything: the Shiplords, in their arrogance and complacence, hadn't envisaged the kind of scenario that was already accounted for and employed on Earth in the 20th century and much earlier. Yes, the Royal Navy at its position of global dominance was backed by the overwhelming might of its numerous ships of the line of battle, but rather than try to cover the world's seas with such fleets, it employed a much greater number of smaller, cheaper, and weaker warships to patrol and be available across the world instead.
The Shiplords falsely equated their mastery over the technology and hegemony over known space with mastery over scale and hegemony over even unknown space. They had the most advanced ships and most advanced industry within known space, but they knew that they were not even remotely close to fully leveraging either their technology or their industry, and just assumed that no one else they might encounter could have developed either the technology or the industry to match them.
EDIT: STill, all that is understandable. What's more egregious is them deciding that the lesson to take away from all that is to be harsher on everyone else and be prepared to fight the threat of the Uninvolved who saved the Shiplords.
EDIT2: Now that I have a minute, I wanted to add that while the Shiplords did learn from some of their mistakes (they have Regular Fleets, they have more contingency plans and reserves, etc), they also made some insane and rather outrageous changes as well, like developing Soulkiller weaponry with the intent of threatening and, if need be, using it against the Uninvolved rather than for the purpose of having a means to fight an enemy that tries to do something vaguely along the lines of what the Hjiven tried to do (something that even the Uninvolved find to be too dangerous to ignore). Being way harsher on the other races--even ones fully willing to listen to the Shiplords--is another inexplicable change because the only ones at fault were the Hjiven, while the other races were either allies or, at worst, helpless against the Sphere without Shiplord protection. This Sorrow is treated as a justification for why First Contact should be done with overwhelming force and uncompromising demands, when the irony is that the reason the Shiplords were in such a bad position in the simulation to start with is because they didn't have the available force prepared to pull that off even if they needed to. And somewhere along the way, First Contact went from "show up with overwhelming force and make commandments to the new species under threat of destruction if they don't comply" to "show up with overwhelming force and commit xenocide, or near-xenocide if they manage to give you a bloody nose before you finish, THEN give commandments...and then return again long before they've even come close to recovering, kick their asses again, make them suffer greatly AGAIN, and keep doing that until they're strong enough to beat the initial force, at which point you alter the commandments a bit but make it clear that you can still destroy them utterly at any time at a whim". (And then psychologically tortue them, bully them, subvert them, and slowly push them towards collective species suicide eventually, as a means of escape from your bullying, only for them to discover that you still have the means to kill them if they ever get uppity, and that their new lifespan is actually relatively short anyway.)
Yeah, there were plenty of lessons from that Sorrow that the Shiplords learned and correctly employed. But the way the Shiplords--even the Hearthguard--talk about it as some kind of foundational justification for all that would follow is utter nonsense that they've somehow convinced themselves of. It also ignores the fact that, with the whole of the galaxy sufficiently explored such that there cannot possibly BE another Hjiven Sphere-like superpower appearing out of nowhere to challenge the Shiplords, rendering such justifications moot.