One theory on why Legendarys cannot seem to reproduce, can because THEY ARE SO RARE. Thoughout the ages of human hunting, war, natural changes, lack of finding good mates or even just the sinple passage of time themselves are all reasons why the Legendaries have hardly any offspring.
Further reasoning why Legendaries cna reproduce is that a Black Shiny Rayquaza appears in of the films, the Legend of Hoopa, implying that there are other Rayquazas that are mostly green, and that some Rayquazas turn black-colored.
Mostly agreed on the general points, but... fungi and plants also have sexes. Though plants mostly have both while fungi are... complicated.
Speaking of, maybe Legendaries just undergo binary fission or budding or just abiogenerate spontaneously as manifestations of nature and other concepts. Sort of like how elemental spirits and personified concepts do in real-life mythology/folklore.