Our recent work has showed that diffractively coupled nanoplasmonic arrays for Fourier transform infrared (FTIR) microspectroscopy can enhance the Amide I protein vibrational stretch by up to 105 times as compared to plain substrates. In this work we consider computationally the impact of a microscope objective illumination cone on array performance. We derive an approach for computing angular- and spatially-averaged reflectance for various numerical aperture (NA) objectives. We then use this approach to show that arrays that are perfectly optimized for normal incidence undergo significant response degradation even at modest NAs, whereas arrays that are slightly detuned from the perfect grating condition at normal incidence irradiation exhibit only a slight drop in performance when analyzed with a microscope objective. Our simulation results are in good agreement with microscope measurements of experimentally optimized periodic nanoplasmonic arrays.