linear="no" attribute exactly for this purpose.
From the epub 2 specification
All OPS Content Documents that are part of the publication (i.e. are
listed in the manifest) which are potentially reachable by any
reference mechanism allowed in this specification must be included in
the spine. Such reference mechanisms include, as a partial list,
hypertext links within OPS Content Documents, and references by the
NCX, Tours and Guide.
For each itemref, the publication author may specify the optional
linear attribute to designate whether the associated OPS Content
Document is primary (linear="yes", which is the default when linear is
not present) or auxiliary (linear="no".) It is important that the
publication author include some kind of internal reference, such as a
hypertext link, to any OPS Content Document that is declared to be
auxiliary; it is recommended that references be added to NCX for all
auxiliary content. At least one itemref in spine must be declared
Specifying whether an OPS Content Document is primary or
auxiliary is useful for Reading Systems which opt to present auxiliary
content differently than primary content. For example, a Reading
System might opt to render auxiliary content in a popup window apart
from the main window which presents the primary content. (For an
example of the types of content that may be considered auxiliary,
refer to the example below and the subsequent discussion.)
Reading Systems are not required to differentiate between primary and
auxiliary content, and for the requirements and recommendations given
in this section may consider all OPS Content Documents in spine to be
primary, regardless of the value of the linear attribute.
This means, all items which are referenced, as footnotes in your case, must be included
in the spine. They can be declared as auxilary, with
linear=no, but it is up to reading
system, how it deals with that.
More advanced readers, like
Readium, works correctly and display auxilary items only on request (link click). Others, like
Calibre in your case, work in the other way.
As I think you use
tex4ht for conversion from
html, you may try to generate inline footnotes, which doesn't make new file for each footnote, but are collected at the end the
html file with:
htlatex filename "xhtml, fn-in"