Welcome to the mine field!
The question is predicated on solving one of the more sensitive dnd-3.5e issues: whether a creature has one unarmed strike or many unarmed strikes, and what that means for the creature's attack routine. To be clear, the core rules do not mandate that a humanoid creature's unarmed strike be with its fist: even a typical nonmonk creature's unarmed strike "may be a punch, kick, head butt, or other type of attack" (PH 121), and a "monk’s [unarmed] attacks may be with either fist interchangeably or even from elbows, knees, and feet" (PH 41). However, other rules artifacts—like the Complete Warrior prestige class kensai (49–52)—imply or even outright state that a humanoid creature makes unarmed strikes—largely exclusively—with its fist, hand, or whatever's attached to the tip of its upper-body dangly bit we call an arm.
To be clear, in the abstract, when outright contradictions arise between the core rules and other rules, the contradictions are typically resolved by the core rules taking precedence—the core rules being the primary source for rules—, and when the core rules are expanded, that rules expansion takes precedence if the core rules are largely silent about whatever's being expanded upon. However, when the rules are simultaneously contradicted and expanded, it's up to the DM to resolve the issue. Such is the case with the prestige class kensai's supernatural ability signature weapon when the kensai picks as its signature weapon unarmed strike. In other words, no matter my opinions on this topic, ask your DM.
This DM would have a kensai use signature weapon as printed
The supernatural ability signature weapon on Imbuing Natural Weapons says
The process for imbuing a kensai’s natural weapons (such as his fists) is the same as for a manufactured weapon, except all of the kensai’s natural weapons of one type are imbued at 100% of the cost + 10% per natural weapon. For example, a human kensai who has Weapon Focus (unarmed strike) may turn his fists into signature weapons for 120% of the XP cost. A six-armed kensai with a bite and tail attack would have to choose between fists, bite, and tail and pay either 160% of the cost (for six fists) or 110% of the cost (for
the single bite or tail). A kensai who imbues a particular type of natural weapon must imbue all his natural weapons of that type (so a human kensai with two fists must imbue both fists). It takes 24 hours for a kensai to imbue one type of natural weapon, regardless of how many actual weapons of that type he possesses. (51)
No matter what other rules arguments ensue, the examples make it clear that the special ability's author really, really wants a creature with multiple fists to pay extra for making its unarmed strike into a signature weapon, other rules be damned, the ability untouched by errata. Although no-fisted, two-fisted, three-fisted, four-fisted, six-fisted, and even hundred-fisted creatures—unless otherwise indicated—all technically have but a lone unarmed strike, the special ability demands such creatures—if they have 1 level of monk, take the prestige class kensai, and pick as their signature weapon unarmed strike—pay different amounts from what another kensai pays for improving his signature handaxe or whatever.
Now, I can't know why the author wants these creatures to pay different amounts for what is, essentially, the same effect, but if it's of any interest, I can offer some raw, utterly unverified speculation as someone whose been playing this game a while: Complete Warrior (Dec. 2003) is probably a transition piece, released a mere 5 mo. after the 3.5 revision to the Player's Handbook. It was likely largely written simultaneously with the revised Player's Handbook and incorporates some rules from the 3.5 revision omitted or changed by the final revision… like, perhaps, a now-absent rule that a creature can make a number of unarmed strikes equal to the number of arms a creature possesses. The author of the special ability signature weapon—unwilling to allow essentially free upgrades on its other weapons—opts to increase unarmed strike prices, and this legacy text remains and continues to plague readers even today. (The bracers of striking (Magic of Faerûn 155–6) (1,310+ gp; 1 lb.), for example, had vaguely alluded to the possibility of enshrining this as a rule years earlier, and Savage Species (Feb. 2003)—a true transition text using some elements of both the original game and the then-forthcoming revision—has its incarnate construct stone golem (120–1) making 2 unarmed strikes—each at its full base attack bonus—for reasons the text leaves unexplained.)
However, despite all this, because it's what the text really does say, this DM would rule that a creature that possesses at least 1 level of monk, that takes levels in the prestige class kensai, and that picks as its signature weapon unarmed strike does, in fact, pay 100% +10% per (ugh) fist like the text's examples say to do. However, this DM would make it clear that such a ruling is made reluctantly, both because the rules here really are a little silly and because this DM's uncomfortable basing game mechanics on the whims of an art department that may've taken artistic license to provide an illustration of a creature that possesses more or fewer arms than the monster's designer imagined.
A player could try to convince the DM that examples aren't rules
This is the argument to make if attempting to convince the DM the description is, in fact, an actual, for-reals mistake. It's a difficult argument to make and it might result in the player who raises it seriously getting dice thrown at him, but it is an argument that carries some weight. Here's how it goes: Only the actual rules are the rules-as-written, and examples of the implementation of those rules are not rules. So, below, stripped of examples, is the relevant section from the ability signature weapon on Imbuing Natural Weapons:
The process for imbuing a kensai’s natural weapons… is the same as for a manufactured weapon, except all of the kensai’s natural weapons of one type are imbued at 100% of the cost + 10% per natural weapon.… A kensai who imbues a particular type of natural weapon must imbue all his natural weapons of that type…. It takes 24 hours for a kensai to imbue one type of natural weapon, regardless of how many actual weapons of that type he possesses.
Thus, as a monk's unarmed strike "is treated as both a manufactured weapon and a natural weapon for the purpose of spells and effects that enhance or improve either" (PH 41)—and this is certainly an effect that enhances—, this means that, technically, a creature that has at least one level of monk and that takes the prestige class kensai and that picks for the special ability signature weapon the creature's unarmed strike—unless the creature has multiple unarmed strike (like that incarnate construct stone golem)—should pay only the 110% cost for imbuing its unarmed strike. (By the way, this reader suspects the extra cost is due to the relative invulnerability and undisarmability of the unarmed strike.) If you make this argument, this fellow player wishes you luck, and may your DM not hurl d4s.
