You can define the secnumformat
separately for each section level by adding a hook to the relevant sectioning command:
\headstyles{bringhurst}
% I don't know what style you're using but chose this one since it
% has italic subsection titles - the same principles apply to any
% set of heading styles.
\setsecnumdepth{subsubsection}
% Make sure subsections are numbered
\let\oldsection=\section
\let\oldsubsection=\subsection
% Save the existing sectioning commands
\renewcommand{\section}[1]{{%
\setsecnumformat{\footnotesize\thesection\quad}%
\oldsection{#1}}}
\renewcommand{\subsection}[1]{{%
\setsecnumformat{{\upshape\thesubsection\quad}}%
\oldsubsection{#1}}}
% New sectioning commands use \setsecnumformat to
% redefine the number font locally. Note the extra
% pair of curly brackets to make sure that the
% \secnumformat returns to normal after the (sub)section
% definition.
Then
\begin{document}
\section{Test me}
\subsection{Another test}
\subsubsection{Test me too}
\end{document}
gives
(the final subsubsection
is to show that we haven't changed the numbering font globally).
(On a typographic note, though, it's possible that what you actually want for section numbers is not small numerals but "old style" ones - if they're available in the font you use.)
Edit
@daleif has pointed out that the cunning extra groups have the unfortunate effect of breaking cross-references. An alternative that avoids this is
\makeatletter
\let\oldsection=\section
\let\oldsubsection=\subsection
\renewcommand{\section}[1]{%
\let\oldsecnumformat=\@seccntformat%
\setsecnumformat{{\footnotesize\thesection\quad}}%
\oldsection{#1}%
\let\@seccntformat=\oldsecnumformat}
\renewcommand{\subsection}[1]{%
\let\oldsecnumformat=\@seccntformat%
\setsecnumformat{{\upshape\thesubsection\quad}}%
\oldsubsection{#1}%
\let\@seccntformat=\oldsecnumformat}
\makeatother
where, instead of defining a group within which the secnumformat
is changed, the old format is explicitly saved and then restored, so that cross-references still work.
I note also that, if you don't care about restoring the old format (i.e., if you're happy to explicitly define a format for every section level you use) an easier method than the first one I showed would be
\setsechook{\setsecnumformat{{\footnotesize\thesection\quad}}}
\setsubsechook{\setsecnumformat{{\upshape\thesection\quad}}}