At least the title, "Endemic Pathogens Are Making You Crazy And Then Killing You", can be accepted as a default prior, rather than an extraordinary claim. Many diseases are both prevalent and not under heavy study. Funding and interest in studying a disease is partially caused by individuals being able to link the disease to a symptom, and this is hard without data. (You rolled a 4, but is the die biased toward 4? It's impossible to tell from a single roll.) When these diseases are occasionally looked into, such as with hookworm and toxoplasmosis, the track record finds harms at an alarming rate, so we should expect the remaining diseases, which are not yet looked into, to have similar rates of danger.

Thus, without making assertions on the article's individual claims, the general thrust is broadly true. The reason people hold the "these diseases are generally harmless" prior is likely from another prior, "if X disease were so harmful, doctors would be studying it", and that unfortunately does not match current practice.

Covid-19 provides an example of how hard it is to link symptoms. We know now that anosmia is solidly connected to Covid-19, but this was not known for a while. The CDC only listed three official symptoms six months after the outbreak [0], reflecting the understanding at the time. Doctors talked about their patients and found commonalities; this bubbled anecdotes into attention. So even with intense and joint attention by the world, with a clear and reliable symptom, the symptom can evade notice for a while. When nobody's attention is on a disease, and the symptoms are chronic, the symptoms become invisible.

Caveat: this is not my field, and I do not study it. An epidemiologist could likely present a more accurate picture.

[0] https://web.archive.org/web/20200415000910/https://www.cdc.g...