Why does the word "nugatory" become nugatory?

Natural selection.

The English language derives from Germanic, French, Greek and Latin roots. This is an explanation for the the many synonyms we have.

Example

Germanic - finger

Latinate - digit

Both of the above survive. We use 'finger' in everyday language. The word 'digit' is used in scientific contexts.

Nugatory has many rival synonyms. Why should it survive? If it is used in a particular context (for example law) then it will survive for that reason. It may be known only within that context -- ordinary people probably never hear it.

If you want to understand in detail how this works, words can be considered to be memes.

Proponents theorize that memes are a viral phenomenon that may evolve by natural selection in a manner analogous to that of biological evolution. Memes do this through the processes of variation, mutation, competition, and inheritance, each of which influences a meme's reproductive success. Memes spread through the behavior that they generate in their hosts. Memes that propagate less prolifically may become extinct.

https://en.wikipedia.org/wiki/Meme