Once pseudo-extension WikibaseJavaScriptApi has become wikibase-javascript-api npm package (i.e. once https://gerrit.wikimedia.org/r/#/c/384025 got merged, tagged, and published on npm), it is no longer installed as a MW extension. As such, it should not pretend to be in its git repo name. Gerrit repo/project mediawiki/extension/WikibaseJavaScriptApi should be renamed (as well as its github mirror).
A possible name for the new location could be wikibase/javascript-api.