Ph.D. is different from other degrees in which you learn and take exams. During your Ph.D. you need a research guide who takes an interest in your work and is involved in active research in the same field as you.
Unless your guide is active in research, they can not guide you. Here research refers to publishable research in good journals.
Your field of research will determine the better option out of the two to pursue your Ph.D. in Economics. If say, you wish to work on Marxism/Communism or related topics, CESP JNU is the right choice for you. You will find ample assistance in JNU.
If you wish to work in Micro Theory such as on Contract theory or Industrial Organization, DSE will be the right option. There are more faculty members in DSE than CITD JNU who work in these areas.
If you wish to work on DSGE literature ( Macro), the guide will exist as a formality and you will be on your own for the most part. This field of research is not pursued by most in India and you will mostly have to rely on yourself.
Also, if you wish to work in the corporate after your Ph.D. , join DSE as it offers very good placements. JNU does not offer on campus placements. The economics at JNU though, is very enriching. There you will be exposed to a variety of subjects, debates, etc.
You must choose between JNU and DSE for your Ph.D. Economics, based on your personal preference and your field of research.
One of my cousins who did a Ph.D. said that choosing a college clearly depends upon the area of interest you have in mind for the research.
Therefore, you need to choose wisely, pursuing Ph.D. would only be good if you receive a good piece of advice from your professors or someone who has appropriate experience.