Ok, I've found it. The problem is that I have something in the xml file that 
produces spurios spaces, which I try to get rid of with \removeunwantedspaces. 
However, this seems to have an effect on the wanted \qquad. 
Is there a way to remove unwanted spaces inside a given element without 
affecting earlier spaces (in other elements) that should appear?
I guess \xmlstrip could be a solution to this problem, but I don't quite 
understand how this works.
Best,
Denis

%%%%%%%%%%%%% Updated Example %%%%%%%%%%%%%%%%%
\startxmlsetups xml:test
  \xmlsetsetup{#1}{*}{-}
  \xmlsetsetup{#1}{index|index-entry|num}{xml:*}
\stopxmlsetups

\xmlregisterdocumentsetup{test}{xml:test}


\startxmlsetups xml:index
    \xmlflush{#1}
\stopxmlsetups

\startxmlsetups xml:index-entry
  \startparagraph
    
\xmlfilter{#1}{/term/command(xml:term)}\qquad\qquad\qquad\xmlfilter{#1}{/loc/command(xml:loc)}
  \stopparagraph
\stopxmlsetups

    
\startxmlsetups xml:term
  \xmlflush{#1}
\stopxmlsetups
    
\startxmlsetups xml:loc
  \removeunwantedspaces
  \xmlflush{#1}
\stopxmlsetups

\startxmlsetups xml:num
  \xmlflush{#1}
\stopxmlsetups

\startbuffer[test]
<?xml version="1.0" encoding="UTF-8"?>
<index>
  <index-entry>
    <term>asdf</term>
    <loc>
          <num>1</num>
         </loc>
  </index-entry>
</index>
\stopbuffer

\starttext

\xmlprocessbuffer{test}{test}{}

\stoptext


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