The CDK addresses this by storing the aromaticity as additional property on the bond:
<bond atomRefs='a1 a2' order='D'> <bondType dictRef="cdk:aromaticBond"/> </bond>
<cml><molecule id="caffeine"><atomArray/><bondArray/></molecule></cml>
<bond atomRefs='a1 a2' order='D'> <bondType dictRef="cdk:aromaticBond"/> </bond>