Sorry, messed up something. New version followws:
\newbox\chemlowbox
\def\chemlow#1%
{\setbox\chemlowbox\hbox{{\switchtobodyfont[small]#1}}}
\def\chemhigh#1%
{\ifvoid\chemlowbox \high{{\switchtobodyfont[small]#1}}%
\else \lohi[left]{\box\chemlowbox}{{\switchtobodyfont[small]#1}}\fi }
\def\finishchem{\ifvoid\chemlowbox \else \low{\box\chemlowbox}\fi}
\unexpanded\def\molecule%
{\bgroup
\catcode`\_=\active \uccode`\~=`\_ \uppercase{\let~\chemlow}%
\catcode`\^=\active \uccode`\~=`\^ \uppercase{\let~\chemhigh}%
\dostepwiserecurse {65}{90}{1}
{\catcode \recurselevel = \active
\uccode`\~=\recurselevel
\uppercase{\edef~{\noexpand\finishchem
\rawcharacter{\recurselevel}}}}%
\catcode`\-=\active \uccode`\~=`\- \uppercase{\def~{--}}%
\domolecule }%
\def\domolecule#1{#1\finishchem\egroup}
\starttext
{\bf A test \variant[Caps] in small caps}
\molecule{HSO_4^{-}}
\molecule{H_2SO_4}
{\bfa A story about \molecule{SF_6}}
{\scx A story about \molecule{sf_6}}
{\bsb A story about \molecule{SF_6}}
\stoptext
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