It wouldn't destroy the universe, only the area around the scub coral (so the whole planet). It has to do with quantum theory and information theory. Thoughts are energy, and too much energy concentrated in one spot can create a rend in space time (black hole). This is show on a small scale at the barrier as time and gravity are null inside it, and the reason it was on a small scale is because only a few scub coral were awaken. The scub coral seem to believe that they can survive entering the black hole whereas humanity would die. After entering the event horizon (black hole) it is just speculative since we don't actually know what can happen. It seems to suggest that the scub coral can jump world lines and reach an alternate dimension via this method.
Actually it's like this -- basically ' The Limit of Questions ' was an homage to American science fiction writer Greg Bear which is referenced by the series character 'Dr. Greg "Bear" Egan' or simply 'Dr. Bear'. The anime character even sort of looks like Greg Bear hehe. Anyway the concept was inspired by Greg Bear's novel Blood Music where the protagonist Vergil Ulam injects himself with intelligent one celled creatures called noocytes (very much like the scub corals).
Soon enough these individually intelligent noocytes multiply inside and make Ulam 'better', also other people become infected and spreads through a considerable population. Eventually the number of these intelligent one celled lifeforms surpasses the human race trillions of times over. So the Earth becomes home to enormous amount of sentient beings. So what is the relation to 'the limit of questions?'
In the Copenhagen interpretation of quantum mechanics, with the strong anthropic principle in mind (that of Barrow and Tipler), conscious observers can collapse a quantum wave function to a particular value of momentum or position. So the sci-fi premise in the novel is that with that humongous amount of conscious intelligent observers 'observing' (and 'questioning' so to speak) the environment and the earth around them, reality will have no room to 'breathe' because it will be pinned down to a particular value, that is, there will be an utter collapse of the quantum wave function everywhere. If reality becomes too 'frozen' or rigid because of too many observers, then reality will break down and the laws of physics will fail. The assumption in the sci-fi novel is that reality needs room to 'breathe' and move freely -- hence the quantum wave function of probability which is intrinsic in the fabric of reality. If the quantum wave function is collapsed on a massive scale because of too many observers then reality breaks down.
In Eureka 7, the 'Limit of Questions' precisely takes on this premise with the scubs in place of Bear's 'noocytes'. That is why the scubs should be in a state of sleep and dreaming to prevent the advent of full consciousness and observation which will trigger collapse. Of course Bear's premise is science fictional in nature, any possible relation to reality has not been proven in the laboratory yet hehe -- of course we don't want to speak hastily and discount anything outright
Both Tengen Toppa Gurren Lagann and Eureka Seven are my all time favorite anime.
And just now I realized that both shows revolve around the same idea of the Anthropic principle.
The main baddies of TTGL want to limit the amount of sentients to prevent the destruction of the universe, and the Coralian also need to go dormant to limit the number of them to not reach that max amount of sentient beings.
Both shows have "antibodies" when that number of beings is near the limit (AntiSpirals for TTGL and Kute-Class Coralian for E7).