Fee Waiver affects admission??

Agree with the above^. You must have your finances, for your full university years, figured out before you apply to the desired schools.
Doing well at a US university is EXPECTED and is the norm. You won’t receive additional funding, after the first year. The universities in the US don’t work that way. Please see this thread:

http://talk.collegeconfidential.com/financial-aid-scholarships/2123602-do-not-assume-that-a-scholarship-will-be-given-to-current-college-student-for-being-on-dean-s-list.html#latest

If you cannot afford the application fees, “right now, during the pandemic”, which are a drop in the bucket compared to the other fees, then you are going to be out of luck the following years as well.