No harm. Everything is not related to tax or worries, unless you have very less or no returns at all. If you earn in lakhs then you are 100% in your rights to deposit few lakhs in NPSWhat’s the harm in paying NPS via debit card?
Other issue might be if you have systematically abused it by using your debit card to pay for many other NPS accounts (to get 2.5% returns and maybe pass on these people 1% discount)