Daaang. Ended up overriding cider-jack-in-clj&cljs via :around advice, and had to add a directory-local var This is my .dir-locals.el:

((nil . ((cider--custom-clj&cljs-jack-in-p . t)
         (cider-shadow-default-options . "app")
         (cider-offer-to-open-cljs-app-in-browser . nil)
         (eval . (progn
                   (defun cider-jack-in-clj&cljs* (&rest params)
                     (interactive)
                     (if (and (boundp 'cider--custom-clj&cljs-jack-in-p)
                              cider--custom-clj&cljs-jack-in-p)
                         (progn
                           (let ((cider-preferred-build-tool 'lein)
                                 (cider-jack-in-default 'lein))
                             (funcall 'cider-jack-in-clj nil))
                           (let ((cider-preferred-build-tool 'shadow-cljs)
                                 (cider-jack-in-default 'shadow-cljs)
                                 (cider-cljs-repl-type "shadow"))
                             (cider-jack-in-cljs '(:cljs-repl-type shadow))))
                       (cl-destructuring-bind (orig-fn args) params
                         (funcall orig-fn args))))

                   (advice-add 'cider-jack-in-clj&cljs :around #'cider-jack-in-clj&cljs*))))))