The problem is basically the same as \pause in tikzpicture breaks footline : on shouldn't use \pause
within a tikzpicture, otherwise bad things will happen.
The solution is just a bit more complicate as the pause is deeply hidden in the smartdiagram code:
\documentclass{beamer}
\usetheme{Warsaw}
\usepackage{smartdiagram}
\makeatletter
\RenewDocumentCommand{\smartdiagramanimated}{r[] m}{%
\StrCut{#1}{:}\diagramtype\option
\IfNoValueTF{#1}{% true-no value 1
\PackageError{smartdiagram}{Type of the diagram not inserted. Please insert it}
{Example: \protect\smartdiagram[flow diagram]}}
{%false-no value 1
\IfStrEq{\diagramtype}{}{%
\PackageError{smartdiagram}{Type of the diagram not inserted. Please insert it}
{Example: \protect\smartdiagram[flow diagram]}
}{}
\IfStrEq{\diagramtype}{descriptive diagram}{% true-descriptive diagram
\begin{tikzpicture}[every node/.style={align=center,let hypenation}]
\foreach \smitem [count=\xi] in {#2}{%
\edef\col{\@nameuse{color@\xi}}
\foreach \subitem [count=\xii] in \smitem{%
\pgfmathtruncatemacro\subitemvisible{\xi}
\ifnumequal{\xii}{1}{% true
\visible<+->{\node[description title,drop shadow, smvisible on=<\subitemvisible->]
(module-title\xi) at (0,0-\xi*\sm@core@descriptiveitemsysep) {\subitem};}
}{}
\ifnumequal{\xii}{2}{% true
\visible<+->{\node[description,drop shadow,smvisible on=<\subitemvisible->]
(module\xi)at (0,0-\xi*\sm@core@descriptiveitemsysep) {\subitem};}
}{}
}%
}%
\end{tikzpicture}
}{}% end-descriptive diagram
}% end-no value 1
}% end-command
\makeatother
\begin{document}
\begin{frame}{Title}
\smartdiagramanimated[descriptive diagram]{
{Step 1,{Defining Step 1}},
{Step 2,{Defining Step 2}},
{Step 3,{Defining Step 3}},
{Step 4,{Defining Step 4}}}
\end{frame}
\end{document}
Another approach could be to patch tikzpicture
(use at your own risk, no idea what other problems this might cause):
\documentclass{beamer}
\usetheme{Warsaw}
\usepackage{smartdiagram}
\AtEndEnvironment{tikzpicture}{\onslide<1->}
\begin{document}
\begin{frame}{Title}
\smartdiagramanimated[descriptive diagram]{
{Step 1,{Defining Step 1}},
{Step 2,{Defining Step 2}},
{Step 3,{Defining Step 3}},
{Step 4,{Defining Step 4}}}
}
\end{frame}
\end{document}