Yes, you simply import them as described here: Removing land by masking - #6 by marjanmarbouti
I don’t know the performance limits of SNAP if you have large amounts of polygons. Do you want to have a plot for each of these thousands of polygons? Can you aggregate them by crop type (dissolve in a GIS)?
I would say, pin points are enough to get an information on vegetation health (NDVI) over a couple of growing seasons. If you can include polygons, even better.