Pro one H1

1. The layout of the headings seem to support this. A page with only one heading that represents the title of the page looks nicer than one with multiple h1.
2. How To Use H1-H6 HTML Elements Properly recommends: "Use Only One H1 Element on any page – even Google recommends this." 

Pro multiple H1

1. H1 is a heading, not a title. Examples from The h1, h2, h3, h4, h5, and h6 elements show that they use multiple h1.
2. HTML5 introduces sections. Maybe this speaks for using h1 headings more than once?

Conclusion

It all boils down to: Should the H1 match the title of the page? If it does, there is only one h1, since there is only one title. If it does not, then you are free to use multiple H1 headings.

And in the end: If we have a topic, say "Animals", and we introduce a section for "References", is this section a subsection of the "Animal" section?

In our documentation we originally to have several H1 as long as these headings refer to technical aspects of the document such as "Abstract", "References", or "Notes". The main topic content is usually aggregated by a H1 of its own. But there are exceptions to this rule, if the author has good reasons.