The claim is that San Francisco's homeless population is generating so much filth and needle waste that the runoff is polluting the bay and ocean. The city disagrees, so the question is whether the lack of evidence will be sufficient to vindicate the city in the minds of those whose anti-homeless prejudices cause them to exaggerate the problem of homelessness beyond the reality that it is largely just an aesthetic problem.
"Hobophobia" sounds like someone mispronouncing, "homophobia" with a cold, but this is the term that comes up when you google, "fear of homelessness." Homelessness does engender real problems, but too often those problems are stoked by the fear, hate, and subsequent malicious treatment of people who are identified as homeless because of clothing, where, or how they live.
A tent, trailer, or makeshift house may seem like inadequate housing to many people, but it can nevertheless be home to the person living there. Proper hygiene and waste disposal are, of course, important and so local governments should facilitate whatever systems of waste disposal are most effective and efficient for people living in whatever way they live.
Alternative waste disposal systems such as composting toilets and other zero-water toilets have been designed and tested for years. Bill Gates' foundation has been challenging us to reinvent the toilet and the UN has even published standards for proper no-water toiletry. Still, traditional aesthetics and prejudices keep local governments biased against alternative waste disposal in favor of more expensive, water-wasting systems that discriminate against low-cost residents of an area.
This Trump EPA accusation of San Francisco holds potential to vindicate the city's homeless population by giving them the chance to prove it is possible to combine hygiene and low-cost living, but if too many 'deplorables' use bad behavior to convince the public that homelessness is deplorable instead of simply an affordable and environmentally-friendly and sustainable lifestyle, they will draw negative governmental attention that will justify unfair treatment of the homeless in the eyes of a less-critical public.
What's more, we should realize that bias against homelessness and low-cost lifestyles in general is the primary cause for discrimination against homelessness. Landlords and others who only value people who make them money resent the homeless and others who manage to live at lower levels of economic dependency. For this reason, businesses and investors may threaten to disinvest in areas that tolerate and/or respect lower-cost lifestyles, and that in turn presses local government officials to oppress and/or evict such residents to satisfy the aesthetics and/or greed of business people (and their paying clients) who can't stand the idea that spending money on their products should be optional instead of a mandatory condition for living in an area.