I can think of three possibilities.
Don't split the equations across lines;
Use \notag on two of the four rows of the align environment;
Use two split environments within the overall align environment.
The first solution looks like it's the simplest overall. Choosing between solutions 2 and 3 will depend, in part, on whether or not the equation numbers should be centered on each of the pairs of rows.

\documentclass{article}
\usepackage{amsmath}
\begin{document}
\hrule
\begin{subequations} \label{eq2}
\begin{align}
\ddot{x}
&= \big( \cos{\phi} \sin{\theta} \cos{\psi} + \sin{\phi} \sin{\psi} \big) \frac{U_1}{m} - \frac{1}{m} \sum_{i=1}^{4} H_{xi} - K_{fdx} \frac{\dot{x}}{m_s}\\
\ddot{y}
&= \big( \cos{\phi} \sin{\theta} \sin{\psi} - \sin{\phi} \sin{\psi} \big) \frac{U_1}{m} - \frac{1}{m} \sum_{i=1}^{4} H_{yi} - K_{fdy} \frac{\dot{y}}{m_s}
\end{align}
\end{subequations}
\hrule
\begin{subequations} \label{eq4}
\begin{align}
\ddot{x}
&= \big( \cos{\phi} \sin{\theta} \cos{\psi} + \sin{\phi} \sin{\psi} \big) \frac{U_1}{m} \notag\\
&\qquad - \frac{1}{m} \sum_{i=1}^{4} H_{xi} - K_{fdx} \frac{\dot{x}}{m_s}\\
\ddot{y}
&= \big( \cos{\phi} \sin{\theta} \sin{\psi} - \sin{\phi} \sin{\psi} \big) \frac{U_1}{m} \notag\\
&\qquad - \frac{1}{m} \sum_{i=1}^{4} H_{yi} - K_{fdy} \frac{\dot{y}}{m_s}
\end{align}
\end{subequations}
\hrule
\begin{subequations} \label{eq4}
\begin{align}
&\begin{split}\ddot{x}
&= \big( \cos{\phi} \sin{\theta} \cos{\psi} + \sin{\phi} \sin{\psi} \big) \frac{U_1}{m} \\
&\qquad - \frac{1}{m} \sum_{i=1}^{4} H_{xi} - K_{fdx} \frac{\dot{x}}{m_s}
\end{split}\\
&\begin{split}
\ddot{y} &= \big( \cos{\phi} \sin{\theta} \sin{\psi} - \sin{\phi} \sin{\psi} \big) \frac{U_1}{m} \\
&\qquad - \frac{1}{m} \sum_{i=1}^{4} H_{yi} - K_{fdy} \frac{\dot{y}}{m_s}
\end{split}
\end{align}
\end{subequations}
\hrule
\end{document}