for Rectangular window if data length is 1K then FFT Length Should be 1K FFT only because ENBW of rectangualr window is 1.0 but for Minimum 4-Sanple BlackmannHarris window is 2.0. so for improving accuracy in terms of either frequency or amplitude which method is preferrded in below 1. for 1K Data i will append 1K zeros and Caluclate 2K FFT or 2. instead of 1K data take 2K data and calclate 2K FFT
or else any other method please calrify ..