I managed to construct an Import
syntax that produces identical results in 11.3 and 12.0. I hope this helps.
Import["http://exampledata.wolfram.com/messier61.fits.gz", {"FITS", "Image", 1}]
I do not know the reason for changing this, but 11.3 already returned an association for a "multi-HDU file" (whatever that means). I guess it was done for consistency: it is useful to have the same result format regardless of file type.