This is because
isearch does not use the minibuffer to read input from the user, rather it simply updates the echo area with the characters entered during
isearch. Please note that the minibuffer and the echo area are different. From the GNU Emacs Manual
The echo area is used for displaying error messages (see Errors), for
messages made with the message primitive, and for echoing keystrokes.
It is not the same as the minibuffer, despite the fact that the
minibuffer appears (when active) in the same place on the screen as
the echo area.
minibuffer-setup-hook is never executed during
isearch since the minibuffer is never setup.
In this specific case,
isearch-mode-map which binds all characters from in ascii range 32 to 255 to
isearch-printing-char which updates the isearch prompt by echoing the new prompt.
If you follow the calls, you will find that
isearch-update is used to update the prompt which
isearch-message-function (if defined) to update the prompt otherwise it falls back to
isearch-message. So a solution might be to set
isearch-message-function to a custom function which calls
message with a propertized string with
face property set to custom face with desired height.
Following implements the idea mentioned in the previous paragraph, most of it is copied directly from the function
isearch-message except for the last part where the string passed to message is propertized to have a larger height.
(defun my-isearch-message (&optional c-q-hack ellipsis)
;; Generate and print the message string.
(let ((cursor-in-echo-area ellipsis)
(fail-pos (isearch-fail-pos t)))
;; Highlight failed part
(setq m (copy-sequence m))
(add-text-properties fail-pos (length m) '(face isearch-fail) m)
;; Highlight failed trailing whitespace
(when (string-match " +$" m)
(add-text-properties (match-beginning 0) (match-end 0)
'(face trailing-whitespace) m)))
(setq m (concat
(isearch-message-prefix ellipsis isearch-nonincremental)
(if c-q-hack m (let ((message-log-max nil)) (message "%s" (propertize m 'face '(:inherit default :height 1.5)))))))
(setq isearch-message-function #'my-isearch-message)