The very best homeless shelter would be to have no shelter at all. Instead, the homeless would go to an office, something like the Social Security office, or the Department of Motor Vehicles.
At this office, the homeless would be given a very thorough assessment of their condition. From all the information gathered, a plan would be created, specific to the needs of the person, a plan that would first get them into a permanent home as quickly as possible, and would then arrange for them all the help they need to address the issues that led them to homelessness. These services, counseling, therapy, abstinance, etc., would be home delivered where they live.
In all the studies conducted so far, this approach is more effective and cost effecient than putting all the homeless into one shelter, and expecting the homeless to solve their homeless situation on their own without assistence.