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I'm using the function rasterToPoints() from the package raster . By default, this function omits the NA values.

raster <- raster(matrix(c(1,2,NA, 1,2,3, 1,2,3), nrow = 3, ncol = 3 ))
raster_points <- rasterToPoints(raster, na.rm = FALSE)
Therefore, I put a raster with 200 cells and I get a data.frame with only 150 rows. How can I obtain the point with empty cells in my final data.frame?
You could combine xyFromCell, values, and cbind.  This returns the central coordinates of each cell (when you initialized the raster, it assumes a 1 x 1 extent unless defined otherwise) and its value, including NAs, in matrix form:
cbind(xyFromCell(raster, 1:ncell(raster)), values(raster))
        
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