There are many ways to plot a file in 3d even though it has only two-dimensional coordinates. One way is to add a column with y=0. Of course, you do not have to do that by hand.
\documentclass[tikz,border=3.14mm]{standalone}
\usepackage{filecontents}
\begin{filecontents*}{data2.dat}
x z
0.5 0
0.54 0.01
0.58 0.01
0.62 0.02
0.66 0.03
0.7 0.03
0.74 0.04
0.78 0.05
\end{filecontents*}
\usepackage{pgfplots,pgfplotstable}
\pgfplotsset{compat=1.16}
\pgfplotstableset{
create on use/new y/.style={
create col/expr={0}}
}
\begin{document}
\begin{tikzpicture}
\begin{axis}[ymin=-0.2,ymax=1]
\addplot3[no marks,smooth] table[x=x,y=new y,z=z] {data2.dat};
\end{axis}
\end{tikzpicture}
\end{document}

Of course, you can also add a smooth plot in the framework you are using.
\documentclass[tikz,border=3.14mm]{standalone}
\usepackage{filecontents}
\begin{filecontents*}{xz.dat}
x z
0.5 0
0.54 0.01
0.58 0.01
0.62 0.02
0.66 0.03
0.7 0.03
0.74 0.04
0.78 0.05
\end{filecontents*}
\usepackage{datatool}
\newcounter{mycoord}
\usepackage{tikz}
\begin{document}
\begin{tikzpicture}[x={(-25.98mm,-15mm)},y={(25.98mm,-15mm)},z={(0,30mm)}]
\draw (0,0,0)--(1,0,0);
\draw (0,0,0)--(0,1,0);
\draw (0,0,0)--(0,0,3);
\DTLsetseparator{ }
\DTLloaddb[noheader=false]{coordinates}{./xz.dat}
\DTLforeach*{coordinates}{\x=x,\z=z}{\stepcounter{mycoord}
\filldraw (\x,0,\z) coordinate(X-\themycoord) circle (0.02);}
\draw plot[smooth,samples at={1,...,\themycoord},variable=\x] (X-\x);
\end{tikzpicture}
\end{document}
Using your data file (and getting rid of the bullets) yields
\documentclass[tikz,border=3.14mm]{standalone}
\usepackage{filecontents}
\usepackage{datatool}
\newcounter{mycoord}
\usepackage{tikz}
%\usetikzlibrary{decorations.markings}
\begin{document}
\begin{tikzpicture}[x={(-25.98mm,-15mm)},y={(25.98mm,-15mm)},z={(0,30mm)}]
\draw (0,0,0)--(1,0,0);
\draw (0,0,0)--(0,1,0);
\draw (0,0,0)--(0,0,3);
\DTLsetseparator{ }
\DTLloaddb[noheader=false]{coordinates}{./xz.dat}
\DTLforeach*{coordinates}{\x=x,\z=z}{\stepcounter{mycoord}
\path (\x,0,\z) coordinate(X-\themycoord);}
\draw plot[smooth,tension=0.5,samples at={1,...,\themycoord},variable=\x] (X-\x);
\end{tikzpicture}
\end{document}

The little wiggles come from the data, not from the smoothening.