Possible:
\pgfplotsinvokeforeach{0,1} {%
\pgfplotstableset{
columns/#1/.style = {
string replace={0}{\pgfplotstablegetelem{0}{[index]#1}\of\test \pgfplotsretval}
}}}%
But this is not so nice, because I have to say \of\test
, so this does not work as a general style...

\documentclass[border=5pt]{standalone}
\usepackage{pgfplotstable}
\pgfplotstableread[header=false]{
A B
1 2
0 2
1 0
0 2
0 2
1 0
}\test
\begin{document}
% Nullen ersetzen
\pgfplotsinvokeforeach{0,1} {%
\pgfplotstableset{
columns/#1/.style = {
string replace={0}{\pgfplotstablegetelem{0}{[index]#1}\of\test \pgfplotsretval}
}}}%
\pgfplotstabletypeset[string type,
skip rows between index={0}{1},% Benennungszeile ausblenden
every head row/.style={output empty row},% keinen header anzeigen
]{\test}
%Test: \pgfplotstablegetelem{0}{[index]0}\of\test \pgfplotsretval
%\pgfplotstablegetelem{0}{[index]1}\of\test \pgfplotsretval
\end{document}
\pgfplotstablegetelem
and\pgfplotsretval
.