There are no problem if you have the EWS certificate and still you can appear for the UP NTSE examination. So you have nothing to worry about and you must satisfy the other eligibility conditions as provided below:

• The candidate must pass the class 9 examination with or above 55% marks for UR and 44% for SC/ST marks are eligible.
• The school must be located in UP
• Open or distance learning students can also apply for the exam.
• Student’s age should be less than 18 years, and should not be employed.

To know more about UP NTSE, visit the link below:

https://school.careers360.com/articles/ntse-uttar-pradesh

I hope this answer helps. All the very best for your future endeavors!