Ghouls and Super Mutants are kinda like Elves: There's always a few of them and they are dwindling, but there's always enough of them.
I suspect there's a few thousand Super Mutants. The Master's OGs probably numbered in the low thousands, say 1000-5000. With Second Gens from Mariposa, there's probably some more.
If you add the East Coast strains (D.C, Huntsville, Commonwealth), I doubt there's more than 7000 Super Mutants altogether. Especially because these creatures seem to be total morons. I suspect there's more brainy East Coast muties than we see in the games (folks like Uncle Leo, Fawkes, etc), but they just leave elsewhere, in order not to be associated with their hurrdurr friends. Huntsville strain is probably long gone, the DC strain was probably hunted down and chased off between Fallout 3 and 4 and the Commonwealth strain is doomed too. Goodbye and good riddance.
There's probably more Super Mutants out there from FEV Quarantine Towns, but I suspect they are insignificant compared to the Mariposa strain.
As for Ghouls... now that we know Ghouls are not a Necropolis one-off, I suspect there's a few million ghouls worldwide, but they are pretty scattered and their numbers far smaller than that of humans. In the post-war US, probably a few dozen or hundred thousands.