I don't know of any easy way of changing the default font used by "Publisher" on the kobo, but you also don't have to change the font individually for each book. When you select a new font, that will the be default for all new books you open.
However, choosing a font with wide Unicode support for those characters will be limited. The problem you are experiencing can be fixed by sideloading your books to the Kobo in Kepub format. (There are lots of threads here, so I'll skip the howto unless it's needed.) People have difference preferences between epub and kepub on the Kobo, but one of the advantages of Kepub is automatic font substitution (which Epub does not.)
PS, the system default font is Georgia
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