Do you really want to use section numbers without chapter number in a scrreprt document?
Here is a suggestion assuming all section levels using sectionlinesformat should be colored:
\documentclass[10pt,
numbers=noenddot% <- added
]{scrreprt}%scrartcl,scrreprt,scrbook
\usepackage[utf8]{inputenc}
\usepackage[T1]{fontenc}
\usepackage{tikz}
\renewcommand*\thesection{\arabic{section}}
\renewcommand*\sectionformat{\thesection.\enskip}
\renewcommand*\thesubsubsection{(\alph{subsubsection})}
\setcounter{secnumdepth}{\subsubsectionnumdepth}
\colorlet{sectioncolor}{red}
\colorlet{subsectioncolor}{blue}
\colorlet{subsubsectioncolor}{green!80!black}
\RedeclareSectionCommands[font=\normalsize]{section,subsection,subsubsection}
\makeatletter
\renewcommand\sectionlinesformat[4]{%
\tikz\node[
inner xsep=1em,inner ysep=1ex,
left color=#1color!20,right color=white,
rounded corners,text=#1color
]{\parbox{\dimexpr\textwidth-2em\relax}{\raggedsection\@hangfrom{\hspace*{#2}#3}{#4}}};
}
\makeatother
\begin{document}
\section{section}
\subsection{subsection}
\subsubsection{subsubsection}
\end{document}

Or assuming all section levels formatted by sectionlevelsformat should use nodes:
\documentclass[10pt,
numbers=noenddot% <- added
]{scrreprt}%scrartcl,scrreprt,scrbook
\usepackage[utf8]{inputenc}
\usepackage[T1]{fontenc}
\usepackage{tikz}
\renewcommand*\thesection{\arabic{section}}
\renewcommand*\sectionformat{\thesection.\enskip}
\renewcommand*\thesubsubsection{(\alph{subsubsection})}
\setcounter{secnumdepth}{\subsubsectionnumdepth}
\RedeclareSectionCommands[font=\normalsize]{section,subsection,subsubsection}
\tikzset{
section/.style={text=red,left color=red!20,right color=white},
subsection/.style={text=blue,left color=blue!20, right color=white},
subsubsection/.style={}
}
\makeatletter
\renewcommand\sectionlinesformat[4]{%
\tikz\node[
inner xsep=1em,inner ysep=1ex,
rounded corners,
#1
]{\parbox{\dimexpr\textwidth-2em\relax}{\raggedsection\@hangfrom{\hspace*{#2}#3}{#4}}};
}
\makeatother
\begin{document}
\section{section}
\subsection{subsection}
\subsubsection{subsubsection}
\end{document}
Now the subsubsections are not colored (as asked in a comment):

If each level should get a different layout, then you have to use nested \ifstr{#1}{<section level name>} commands:
\ifstr{#1}{section}
{<code for sections>}
{\ifstr{#1}{subsections}
{<code for subsections>}
{<code for all other levels>}
}%
Example:
\documentclass[10pt,
numbers=noenddot% <- added
]{scrreprt}%scrartcl,scrreprt,scrbook
\usepackage[utf8]{inputenc}
\usepackage[T1]{fontenc}
\usepackage{tikz}
\renewcommand*\thesection{\arabic{section}}
\renewcommand*\sectionformat{\thesection.\enskip}
\renewcommand*\thesubsubsection{(\alph{subsubsection})}
\setcounter{secnumdepth}{\subsubsectionnumdepth}
\RedeclareSectionCommands[font=\normalsize]{section,subsection,subsubsection}
\tikzset{
sectionlinesformat/.style={
inner xsep=1em,inner ysep=1ex,
rounded corners
}
}
\makeatletter
\renewcommand\sectionlinesformat[4]{%
\ifstr{#1}{section}
{\tikz\node[sectionlinesformat,left color=red!20,right color=white,text=red]
{\parbox{\dimexpr\textwidth-2em\relax}{\raggedsection\@hangfrom{\hspace*{#2}#3}{#4}}};}
{\ifstr{#1}{subsection}
{\tikz\node[sectionlinesformat,left color=blue!20,right color= white,text=blue]
{\parbox{\dimexpr\textwidth-2em\relax}{\raggedsection\@hangfrom{\hspace*{#2}#3}{#4}}};}
{\@hangfrom{\hspace*{#2}#3}{#4}}%
}%
}
\makeatother
\begin{document}
\section{section}
\subsection{subsection}
\subsubsection{subsubsection}
\end{document}
\arabic{subsubsection}if you want it to be(\alph{...})? – TeXnician Feb 09 '17 at 21:29\arabic{subsubsection}, I don't have what I expect. – Stan Feb 09 '17 at 21:31