Not a stupid question at all. The reason that there are nine squares may be just because it's bigger, cooler and still symmetric to use nine squares for the most special saving point in the game. It basically forces you to save there and it also warns that something big is going on. This may be the reason that nine squares is used in the game. You probably knew this and this wasn't quite what you were asking so here is a little explainatory on the subject:
Number nine
So, I did a little search concerning the subject, nine - the number of Satan. I found this.
http://www.geocities.com/Paris/Bistro/1368/666913.html
"And they both keep on infinitely multiplying & adding up to NINE. Satan's number. The number of the EGO, as it keeps returning unto itself. As a study of "The Unknown Known" shows, Satanic Forces work in variables of Nine --- Epochs & Ages. Keeping this in mind, also consider multiples of Nine in seconds, minutes, hours, Days, Months {as in Pregnancy, the genesis of Life}, Nine Years, etc.
Satan represents the flesh, carnal desire, all the considerations of the physical aspects of existence. Of material attainment. Satan is the body, with all its lusts, & which houses the brain, the wellspring of creation. As Nine signifies Satan, consider this...there are NINE bio-systems in the body, which comprise your being! Indeed, the sinews of Satan moving your flesh! No wonder blindlighters attempt to thwart themselves! To be purely Natural is the epitome of strong life!
THE NINE BIO-SYSTEMS
I. Skeletal.
II. Muscle.
III. Nervous.
IV. Digestive.
V. Repiratory
VI. Circulatory.
VII. Lymphatic.
VIII. Endocrine.
IX. Reproductive."
What comes to two pyramid heads...
"2
An the Qaballah, the number deliniated unto Satan as Promethius, is 2. Promethius is the Greek God who brought down the bliss of fire & light unto man. Lucifer's equivalent. He is also equivalent to Azazel, as He also brought the knowledge of cosmetics, & unto Abaddon, with the weapons of war.
A comparison can also be made with the serpent of Eden, who, of course, offered man the "knowledge of 'good & evil'", & the promise that Adam & Eve would "be as gods". Satan has always been man's greatest companion. Although man has, since xianity, been a miserable ingrate {Refer to the 4th Satanic Statement}. Throughout all mythology, there has always been the manifestation of Satan in on form or another. He always offers divinity, "forbidden" {the "f-word" for Satanists} & occult knowledge, & liberation from the stagnant tyrannical gods who would prefer to keep mankind in ignorance & subjection. Lucifer is always there, offering earthly delights to those with the courage to accept.
2 signifies Baphomet's horns thrust upwards in defiance, in bold rejection of servility. "God" skewered on the points.
The unity of the bestial & the civil in man, thus attaining the balance of the emotions & the intellect. Love & Lust, Love & Hate, Darkness & Light, Pain & Pleasure, The Macrocosm & The Micsocosm {"As above, so below"}, fantasy & reality ----- all these in equilibrium, one complimenting the other."
Perhaps it's not a coincidence like I originally thought.