First, in general, Isearch uses the minibuffer only for `M-e`.  So your `minibuffer-local-isearch-map` key binding is useless here.  That's the keymap used when editing after `M-e`.

Second, your `isearch-mode-map` binding means that `C-h` ends up deleting the char in the buffer you're searching, not deleting a char from the search string. The current buffer remains the buffer you're searching.

This is what you need to do. It defines a command that pops the last char off of the end of the search string.

``` lisp
(defun foo ()
  "Delete last char of the search string."
  (interactive)
  (unless (equal isearch-string "") (isearch-pop-state))
  (isearch-update))

(define-key isearch-mode-map (kbd "C-h") 'foo)
```