There is no absolute answer to the question. It varies from school to school. The party line is that the admissions process is completely separate and independent from the ROTC selection process. However, there were some colleges my son applied to where the unit representative informed us that, once he found out he received the scholarship, he would immediately inform the admissions office and that it was greatly considered. Others informed us it was not considered at all. Generally speaking, the more selective the college, the less weight was given to the NROTC scholarship selection. Some NROTC units will tell you that it can only help if that school is your #1 choice on your NROTC application.
The bottom line is, it depends.