begin{filecontents}{jobname.cls}
    ProvidesClass{jobname}[2018-11-20 v1.0 SE Test package]
    RequirePackage{pgfopts}
    pgfkeys{
        testproj/.cd,
        mystuff/.store in = myValue,
        mystuff = {} % <-- Set default to empty
    }
    ProcessPgfOptions{/testproj}
    LoadClass[myValue]{scrartcl} % article is working
    endinput
end{filecontents}
documentclass[mystuff={hello=SE,test=1}]{jobname}
%pgfkeys{/testproj/mystuff = {hello=SE}} % <-- working as aspected
begin{document}
    myValue: myValue
end{document}

begin{filecontents}{jobname.cls}
    ProvidesClass{jobname}[2018-11-20 v1.0 SE Test package]
    RequirePackage{pgfopts}
    pgfkeys{
        testproj/.cd,
        mystuff/.store in = myValue,
        mystuff = {} % <-- Set default to empty
    }
letzzz @expandtwoargs
def@expandtwoargs#1#2#3{%
  edeftmp@zz{noexpandzzznoexpand#1{noexpanddetokenize{#2}}{noexpanddetokenize{#3}}}%
   tmp@zz}
    ProcessPgfOptions{/testproj}
    LoadClass[myValue]{scrartcl} % article is working
    let@expandtwoargszzz
    endinput
end{filecontents}
documentclass[mystuff={hello=SE,test=1}]{jobname}
%pgfkeys{/testproj/mystuff = {hello=SE}} % <-- working as aspected
begin{document}
    myValue: myValue
end{document}