I need 6-hour MERRA-2 reanalysis data to do some research. I downloaded the data from this website: https://disc.gsfc.nasa.gov/datasets/M2I6NPANA_5.12.4/summary?keywords=merra
TL;DR: It is not a problem, it is a feature.
As it was pointed in the comments, 1000 hPa over land (and sometimes over ocean) is below the surface. MERRA is just fair enough not to put any values where they do not exist. Other reanalyses use some procedure to fill the gaps and make fields without holes. The procedure is reanalysis specific, and, can ususlly be found in corresponding technical manual. The gap-filled fields have little physical meaning anyway.
If the gaps do not make sense for you, 1000-hPa wind is, probably, not the field you need. E.g. if you are after near-surface wind, 10-m wind is more appropriate quantity.