Just to add to egreg's fine answer. Why it moves up? TikZ will center the enclosing box, as is obvious from the image below:
TeX aligns the letters symbols at their baseline in text mode and at a centerline, if they are in maths mode. Kerning is a partial solution as egreg, showed. Having the +
in math is a better solution. It is not just a font issue, but also the way TikZ aligns which is closer to mathmode. Better even design a small cross using TikZ and have it placed at the exact center.
\documentclass[border=3mm]{standalone}
\usepackage{tikz}
\def\boxes{\fbox{\fbox{y}\fbox{x}\fbox{+}\fbox{f}}}
\begin{document}
\begin{tikzpicture}[
or/.style = {circle,
minimum size=6mm,
very thick,
draw,
font=\ttfamily,
},
]
\node[or,font=\normalfont] (a) {yx\textsuperscript{2}+};
\draw[very thin,red] (a.west)--(a.east);
\node[or] (b) at (1.3,0) {$x^2_3+$};
\draw[very thin,red] (b.west)--(b.east);
\fboxsep0pt\fboxrule0.1pt
\node[or] (c) at (2.5,0) {\fbox{\fbox{y}\fbox{x}\fbox{+}}};
\draw[very thin,red] (c.west)--(c.east);
\end{tikzpicture}
\texttt{\boxes}
\end{document}
+
because TeX doesn't know about this two lines which make up the plus.