I would like to make a publication available as a subpage of my Wordpress site. Therefore I would need the Next/Previous links or arrow buttons for this subsection of the pages [not posts] (or, nevermind, for all pages).

At the end of a WP Codex page (http://codex.wordpress.org/Next_and_Previous_Links) there is a piece of code for that but in case of Atahualpa I have no idea where should I stick it.

I could use either of the plugins referred there (although seemingly not supported any more), but these require adding the codelines to the template as well. Whereas there is no page template in atahualpa at all.

Any suggestions?

if you use the 'Next Page' plugin you just put two shortcodes in each page
[previous][next]
for it to work. I f you want it supported you should contact the plugin author and donate to her.

You could dig thru the theme code and code a solution. If you do let us know and if it looks good we can include it in the next version of the theme.