Read the Ordinance , boys; thoroughly, this time. There is nothing in the ordinance that specifically makes homelessness illegal; there is only the stated declaration to keep its public rights-of-way clean and available for public use, and to protect the public health, safety, and access by City constituents.
People are is still free to be homeless; they are simply no longer allowed to exercise that freedom to occupy streets, sidewalks, alleys, doorways, parks, parking lots, recreational areas, overpasses, underpasses, freeway ramps, or rights-of-way for public utilities.
Homelessness itself is not always the fault of the homeless person, so it cannot -- and should not -- be a crime. Trespassing, blocking traffic, and preventing free and easy access of public spaces to others (especially the handicapped) is and should be unlawful.
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The mere fact that science may not yet adequately explain an object, event, or experience does not mean the immediate explanation should automatically default to a conspiratorial, extraterrestrial, paranormal, or supernatural cause.