This is a seed for further articulation on why EA should rate the importance of biodiversity higher:
Focusing on human x-risk implicitly assumes that there is something uniquely valuable about being human or having human experience. But then, why should we assume that there is nothing uniquely valuable about the existence of any of the other millions of species that inhabit our planet? We know very little about the experience of other species - the limited information on what we do know is obviously filtered through human eyes, so we are potentially ignorant of a whole range of experience that other species may have, but we do not. Yes, ground beetles cannot build rockets and have no potential for colonizing our local cluster of galaxies, but it is our pre-conditioning human experience, our bias, that allows us to totally dismiss the inherent value of the existence of ground beetles.
As has been mentioned many times before, EA overrepresents welfarist/utilitarian frameworks, which to begin with, hold the individual human as a moral agent, and then defines everything else as a moral patient worthy of consideration using the yardstick of human experience of pain and pleasure. Yes, in this framework, biodiversity is most likely of limited utility. But again, this is NOT the only 'valid' ethical lens out there, and there are many arguments out there for why the basic assumptions are dubious. If aliens exist, perhaps they could have no understanding of pleasure or pain, or otherwise be supersentient, such that we are as relatively conscious as an insect.
If one were to assume the system itself as a 'moral patient' (as some cultures do), then irreversibly removing parts of the system is causing harm to it. Maybe including something as abstract as a 'system' in the circle of moral concern sounds absurd, but again, many cultures, among Indigenous Americans, for example, held that even the well-being of the whole system of plants, animals, and people was worthy of consideration.
Depending on your moral framework, protecting biodiversity is an incredibly urgent and neglected cause area, as the magnitude and speed at which it is happening is great (estimates up to 30% total loss just in this century). There is also, as other commenters spoke to, enormous potential to apply EA-style thinking to this problem. To end with an opinion, protecting biodiversity for the sake of biodiversity is the epitome of the word altruism, as it is outside considerations of utility for ourselves or our progeny (through which we like to imagine ourselves as vicariously living after our death).
Partially the answer to this question is that biodiversity protection involves a wide variety of interventions, some presumably effective, some not, and across all those interventions it is not clear how neglected the cause area actually is.
However, a bigger reason might be the inherent conflict between traditional environmental protection, focusing on biodiversity, and the animal welfare/liberation movement. The latter is a lot more prevalent in effective altruism, through organizations like Animal Charity Evaluators and Wild Animal Initiative. There are some sources I can recommend to help clarify the nature of this conflict, starting with "A Triangular Affair" by J Baird Callicott, and "In Nature's Interests?" by Gary Varner, but briefly: if wild animals are moral patients with rights, it is not clear that their status as this-or-that-endangered-species matters very much, and vice versa. In EA, we tend to focus on the experience of animals as a neglected source of suffering, and that does trade off against biodiversity concerns.
Finally, the philosophical case for why we should value biodiversity isn't clear-cut, although I certainly share your intuitions about it! This is an essay from a biologist in the community about what might be valuable about biodiversity and how mainstream environmentalism might be getting it wrong: https://eukaryotewritesblog.com/2018/05/27/biodiversity-for-heretics/