A bit more info (and weirdness).  So, I decided to take a look at it myself, stripped down my project and  pulled in 0.12.985 directly.  Running the following in the REPL gives me the same issue:
(require '[clojure.tools.deps.alpha :as deps])
  (require '[clojure.tools.deps.alpha.util.maven :as mvn])
  (deps/resolve-deps {:paths ["src" "resources"]
                      :deps  '{org.clojure/clojure              {:mvn/version "1.10.3"}
                               com.datomic/ion                  {:mvn/version "0.9.50"},
                               software.amazon.awscdk/codebuild {:mvn/version "1.115.0"}}
                      :mvn/repos
                             (merge mvn/standard-repos {"datomic-cloud" {:url "s3://datomic-releases-1fc2183a/maven/releases"}})} {})
But.. I then pulled the tools.deps.alpha code,  and ran the same thing in the Rich Comment Block, and it works fine. 
 (print-tree
    (resolve-deps {:paths ["src" "resources"]
                   :deps  '{org.clojure/clojure              {:mvn/version "1.10.3"}
                            com.datomic/ion                  {:mvn/version "0.9.50"},
                            software.amazon.awscdk/codebuild {:mvn/version "1.115.0"}}
                   :mvn/repos
                          (merge mvn/standard-repos {"datomic-cloud" {:url "s3://datomic-releases-1fc2183a/maven/releases"}})}
      {}))
 I first assumed that it'd been fixed on master, but even checking out the 0.12.985 tag, and rerunning it seems to be fine.    In my test project, making tools.deps a :local/root or :git/url based dep results in it working as expected.  
So I'm assuming that maybe there's some weirdness in the CLI.jar itself.  I tried upgrading to the latest 1.10.3.929, but the issue persists via the CLI