Simply conducting the experiment myself, this seems to work perfectly fine. But your results may vary, so save a back-up of your mirc.ini file.

Code:
; To clear the CTRL+F find history in mdi windows.
//remini $mircini find2

; To clear the CTRL+F find history in script editor.
//remini $mircini find

; Optional.  Just to be sure.  Also type:
/saveini