You could make your own wrappers around async-shell-command and shell-command to autofill with your last command + have your whole history. Try the code below to see if it does the job like you'd like.

(defvar async-shell-command-history nil
  "List of commands executed with `async-shell-command`.")

(defvar shell-command-history nil
  "List of commands executed with `shell-command`.")

(defadvice async-shell-command (before save-command-in-history activate)
  "Save the command executed with `async-shell-command` in its history."
  (let ((command (ad-get-arg 0)))
    (unless (string-blank-p command)
      (setq async-shell-command-history (cons command async-shell-command-history)))))

(defadvice shell-command (before save-command-in-history activate)
  "Save the command executed with `shell-command` in its history."
  (let ((command (ad-get-arg 0)))
    (unless (string-blank-p command)
      (setq shell-command-history (cons command shell-command-history)))))

(defun my-async-shell-command ()
  "Run `async-shell-command` with a choice from its command history."
  (interactive)
  (let* ((command (completing-read "Async shell command: "
                                   async-shell-command-history
                                   nil nil
                                   (car async-shell-command-history)))
         (final-command (if (string-blank-p command) 
                            (or (car async-shell-command-history) "")
                          command)))
    (async-shell-command final-command)))

(defun my-shell-command ()
  "Run `shell-command` with a choice from its command history."
  (interactive)
  (let* ((command (completing-read "Shell command: "
                                   shell-command-history
                                   nil nil
                                   (car shell-command-history)))
         (final-command (if (string-blank-p command) 
                            (or (car shell-command-history) "")
                          command)))
    (shell-command final-command)))