I'm not sure this is something more general in the MathML module or if it's
specific to the vertical bar in this particular context, but here is a
minimal example showing that the "=0" at the end of the equation is
disappearing:

\usemodule[mathml]
\starttext
\xmlprocessdata{}{<imath>
        <math xmlns='http://www.w3.org/1998/Math/MathML'>
          <mi>A</mi>
          <mfenced open="(" close=")" separators="">
            <mi>B</mi>
            <mo>|</mo>
            <mi>C</mi>
          </mfenced>
          <mo>=</mo>
          <mn>0</mn>
        </math>
      </imath>}{}
\stoptext

And here is a workaround using <mtext> instead of <mo> for the vertical bar
which makes the "=0" magically reappear again:

\usemodule[mathml]
\starttext
\xmlprocessdata{}{<imath>
        <math xmlns='http://www.w3.org/1998/Math/MathML'>
          <mi>A</mi>
          <mfenced open="(" close=")" separators="">
            <mi>B</mi>
            <mtext>|</mtext>
            <mi>C</mi>
          </mfenced>
          <mo>=</mo>
          <mn>0</mn>
        </math>
      </imath>}{}
\stoptext

Flagged up mainly in case it is a bigger problem than just vertical bars in
this specific context.

Thanks,

Duncan