Probably not as rare as you think, they just dont come up for sale often as the owners know what they have and just run them forever, i know of several local to me, more manuals than autos actually, Same with the 80 series tbh, loads of manual ones around but rarely see one up for sale, usually an auto or a petrol. people dont hold on to the autos or petrols as much because of how bad on fuel they are compared to the diesel manuals. most of the 100s around here have had the AHC removed, which is a surprisingly easy job tbf
Know of a secondhand machinery dealer who will only buy manual Landcruiser as his vehicle. Does over 50K miles a year but says they are becoming harder and harder to find them in spec he wants with the manual box.
Think his last one was well over 400k miles when he got his current one with just 150k on the clock.
Those that have them definitely reluctant to give them up.