For calculation of 75% for JEE, the 5 main subjects are taken into consideration. But if the student has failed in any of the main subjects and appeared for any additional subject, then in place of marks of failed subject, marks of that particular additional subject are taken into consideration.

But since the board criteria for admissions to IIts has been removed, it is much highly likely that admissions to NIts will also be taken without making use of board marks of the candidates. However, the final decision is yet to be made. So, keep visiting the official website of NTA and be informed.

Hope it helps.