Deps may be well documented, but lots of introductory material seems to use lein. Having two systems is more confusing.
More and more introductory material is appearing these days featuring deps.edn but given there was a decade of Leiningen usage out there before deps.edn even appeared, the current state of affairs shouldn't surprise anyone.
As for more than one system, lots of languages have that situation: consider make -> ant -> maven -> gradle etc.