Hi Prasad,
Where the data resides should be based on what is the source of truth.
Keeping the data within AEM is always better considering the performance, network latency etc..
However, if this is the common content which needs to be accessed by multiple systems, then its better to keep it in RDBMS itself.
Migration:
Irrespective of whether the data is structured or unstructured, once you have the information architecture defined in AEM, you should be able to create a one time script and migrate the data from DB to AEM.
Thanks,
Lokesh