While I'm not familiar with any of the packages of that nature, I've had a quick look at the package documentation and code for invoice and I believe there is no 'in-built' mechanism to do this. However, I have come up with a quick hack (based on the current version of invoice.sty and liable to break) which simply omits printing of these subtotals (but still calculates them). I'm not quite sure if a solution with such a result is acceptable to you, or if you still wish to get subtotals when they actually provide some meaning? (The latter would be possible but more involved.)
So here's the hack (and I apologise because it is ugly), and I should also add the disclaimer that while I think it doesn't change the calculations, you should probably convince yourself of this too:
\documentclass[11pt]{letter}
\usepackage{invoice}
\makeatletter
\renewcommand{\Print@ST@Fees}{%
\gdef\Flag{4}%
%\SubtotalFee & & & &% print the subtotal of fees
% \Print@Value{\theST@Fee}\\%
}%
\renewcommand{\ST@Project}{%
\gdef\Flag{7}%
\\
%\SubtotalProject & & & &
\addtocounter{ST@Project}{\theST@Fee}%
\addtocounter{ST@Project}{\theST@VAT}%
\addtocounter{ST@Project}{\theST@Expenses}%
% \Print@Value{\theST@Project}\\
}
\renewcommand{\Tot@l}{%
\\\hline
\ifnum\theFee>0 %\SumFees& & & &%
%\Print@Value{\theFee}\\
\ifVATnonzero%
\Total@VAT@Printout%
\fi%
\fi%
\ifnum\theExpenses>0 \SumExpenses& & & &%
\Print@Value{\theExpenses}\\
\fi%
\ifnum\theDiscount<0 \Discount@Contents& & & &%
\Print@Value{\theDiscount}\\
\fi%
\hline\hline
\textbf{\Total} & & & &%
\message{^^J\Currency: \BC}%
\message{^^J\VAT: \VAT@rate}%
\addtocounter{Total}{\theFee}%
\message{^^J\SumFees: }\Message@Value{\theFee}%
\addtocounter{Total}{\theVAT}%
\message{^^J\SumVAT: }\Message@Value{\theVAT}%
\addtocounter{Total}{\theExpenses}%
\message{^^J\SumExpenses: }\Message@Value{\theExpenses}%
\ifnum\theDiscount<0 %
\addtocounter{Total}{\theDiscount}%
\message{^^J\Discount@Contents: }\Message@Value{\theDiscount}%
\fi %
\textbf{\Print@Value{\theTotal}}%
\message{^^J\Total: }%
\Message@Value{\theTotal}\message{^^J^^J}\\%
\end{longtable}
%\end{center}% Removed 20050621 by suggestion from ...
\gdef\Flag{8}%
}
\makeatother
\address{123 derp }
\signature{D}
\date{10-10-2012}
\begin{document}
\begin{letter}{ }
\opening{Invoice no. }
\begin{invoice}{USD}{0}
\ProjectTitle{}
\Fee{herp} {50} {2}
\Fee{derp}{50}{5}
\hline
\end{invoice}
\end{letter}
\end{document}
If you find this answer isn't satisfactory, see what answers others are able to provide and/or consider contacting the package maintainer.