In no literary work by him or pertaining to his life has it been said that he crossed his eyes in combat, or at least in a literal sense as you have taken it. I have been a long time student of Japanese history and have read the actual Japanese text of Go Rin no Sho (The Book of Five Rings) and nowhere in it does it state this. You have either read a bad translated peace or have misinterpreted the text.
Also, I should state, as a long time practitioner of Niten-Ichi swordsmanship (the style Musashi founded) there has never been mention of such eye crossing which further debunks your interpretation.
You must use a critical mind when reading such stuff. It should be quite apparent that when using a close range focus (which is basically what going crossed eyed is) will not in anyway aid your ability to conduce combat. It will be nothing short of a great disadvantage, both attributes of blurred and duel vision would be a great impediment.
It's called a placebo effect. It is all in your head, since you heard that some great swordsman from century ago had apparently used such a tactic you let your brain lead you to believe that it actually works, when in essence it is not.
Unfortunately the historical record shows that he has never stated such a thing.