Your question set me wondering as well. All these sex toys were certainly prevalent by mid Edo Period, with specialty sex toy stores serving the shogun’s capital of Edo. I’d bet my bottom dollar James Clavell was familiar with ukiyo-e prints such as this one: Illustration of a collection of sex toys for women.
Not to mention shunga art in which the toys are being used.
The British Museum has a box of early 20th century Japanese women's sex toys with accompanying text explaining their names and uses. These exact sex toys appear in Edo Period art and texts.
Can these Edo Period sex toys be pushed back to the period of Clavell’s novel, though? Shogun begins in 1600, with the arrival of its main character in Japan. 1600 is the start of the Edo Period, and in fact the novel deals with a fictionalized version of the events that launched the era. Would the sex toys in the novel exist in 1600 Japan? I’ve come to the tentative conclusion that yes, they did exist, but possibly not in the precise manner that Clavell presents them.
The sex toy scenes in Shogun are actually discussed in the chapter “Consorts and Courtesans: The Women of Shogun” by Henry Smith in Learning from Shogun Japanese History and Western Fantasy ed. Henry Smith, 1980. - Columbia university hosts the whole book for free!
The ingenious sexual devices which Kiku displays for the astonished Blackthorne (pp. 694-5) are also essentially Chinese in origin (although the Chinese themselves preferred to insist that all such mechanical aids were of barbarian origin!), but came to be used as well within the pleasure quarters of Tokugawa Japan. As for “harigata” (in Japanese, normally harikata) or dildos (p. 693), it is very unlikely that a high daimyo lady in the year 1600 would be as accustomed to such instruments as Mariko appears to be, but they did come to be used a century later in the shogunal harem by the many women (attendants, maidservants, and even consorts themselves) who were isolated from men on pain of death. In the era of Shogun, available evidence suggests that harikata were used primarily for the training of male prostitutes, and perhaps for the use of their Customers.
Note how Smith suggests that the use of sex toys existed c. 1600 but that they had become much more popular by a later era. With that in mind, I’ve been looking for references to sex toys in the early Edo Period, wondering when they do begin to appear commonly.
I can’t say I’ve done a deep search of Japanese literature, but was amused to find that The Life of an Amorous Man (Kōshoku Ichidai Otoko), written in 1682, ends with the dissolute hero sailing off to find the legendary island of women, a bunch of sex toys stored on board.
A little bit more practically, Yoshida Hanbei’s 1686 Kōshoku Kinmō Zu has some claim to be Japan’s first encyclopedia of sex education, detailing everything from anatomy to sex positions to how to behave on a visit to the Yoshiwara.
Alfred Haft writes of Yoshida’s book:
After an essay on male-male intercourse, and another discussing the shapes of male and female sexual organs, Hanbei provided illustrations of "Paraphernalia" (kizai), which range from ordinary things found in a woman's bedroom or dressing room (mirror stand, make-up jars, clothing, etc.), to sex toys (such as strap-on dildos), to a grocery section, which illustrates some of the foodstuffs recommended to restore energy after lovemaking: burdock root, yams, eggs, loach, and eels.
(The entire essay is well worth reading for a view into the era’s attitude towards sex.)
These references are about eighty years after the novel Shogun is set, but if by the 1680s, the use of sex toys is so ubiquitous and celebrated, it would be no surprise if such sex toys were in some contexts in use in 1600.
Smith particularly doubts if a daimyo’s lady such as Mariko would be accustomed to sex toys, in the way that Clavell presents. Perhaps not, but I want to share a bit of very popular literature from 1748 that may not pertain to a lady in 1600, but might explain why Clavell could make the association.
In an essay on shunga (erotic prints) audiences in Japan, Hayakawa Monta writes:
The common contemporary “polite” view of pornography in Japan is that it is obscene and tends to be aimed at lecherous men, but there are a considerable number of sources from the Edo period that suggest that women too were fans of shunga. One early example from 1748 is from the jōruri 浄瑠璃 (and later kabuki) play Kanadehon chūshingura 仮名手本忠臣蔵 (Treasury of Loyal Retainers), based on the actual 1703 samurai vendetta of the forty seven rōnin. There are some interesting lines spoken by the merchant Amakawaya Gihei, who is helping the rōnin obtain weapons. He has hidden the weapons in some large chests and is preparing to load these onto boats for transporting from Osaka to Edo. At this point enemy soldiers arrive and demand to inspect the chests.
When the soldiers try to open the chest, Gihei runs up and kicks them, and plops down on top of the chest with his legs crossed. He declaims: “This long box contains personal articles ordered by the wife of a certain daimyo, including shunga books and sex toys. Her name is written on each article, even on the order for the erotic materials. If you open the box you will be exposing to public view the name of a great family. And seeing this name may endanger your lives.”
After hearing Gihei’s words, the soldiers withdraw, but the point to note here is that the soldiers believed Gihei, that a daimyo’s wife could be a customer for erotic books and sex toys. is implies that the audience of the time would also accept this assumption as being true. We can conclude that whether it was true or not, it was commonly expected that highborn ladies would be interested in and enjoy shunga, even if they wished to keep this from public view.
Anecdotes such as these about Edo Period women of status may have moved Clavell to project backwards to 1600 with the lady Mariko. And who knows? Perhaps he's right. There certainly is just a lot more textual evidence for bedroom customs a century later, but the explosion of Edo Period literature regarding every facet of ordinary life doesn't mean none of those facets weren't around earlier.
To add on to this, is there any actual evidence of courtesans using yoni eggs? They're all sold with this backstory of being used by royal courtesans for centuries blah blah blah
Somewhat related follow-up question: Is there any evidence of the use of rope bondage for sexual purposes during this time period? We know that martial arts of the time had curricula for tying people (hojojutsu). To what extent were people who knew these techniques also using them in the bedroom?