Hello Iam,
Yes that would be useful I think.
The problem is that it is not so easy. JME is build on shortanswer and answers are stored in the same answers table. In this table there is no field to store the structure and as I understand it it is not possible to construct the structure from the SMILES representation.
So what would be needed would be to use another linked table with an additional field (extra_answer_fields). Quite some work and many places to modify.
Unfortunately this is unlikely to happen before summer as I am already struggling to finish my work on the formulas question type.
But I suggest you create an issue in CONTRIB tracker so that I don't forget this.