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In other words, it was only a problem because lucrative business opportunities financially profitable to risk the voyage under less than ideal conditions year round.

In other words, it was only a problem because lucrative business opportunities made it financially profitable to risk making the voyage under less than ideal conditions year round.

On the other hand, the sengokubune were relatively small vessels operated by only 15 people each.

The question mentions "90 episodes listed by Hidetoki" - that is a death toll of perhaps at most 1,350 (in practice, many of the ships would've survived afloat, but rudderless). In 1703 alone a single storm in the English Channel killed over 1,500 sailors. So in comparative terms, judging by the currently presented evidence at least, Tokugawa shipping does not seem unusually costly.

For context, there was as many as 1,400 voyages per year on the aforementioned Osaka-Edo route by the higakikaisen cargo ships around 1700.

元禄時代には 1 年に最大のべ 1400 隻の菱垣廻船が大坂・江戸間の輸送に従事した

In the Genrokue Era each year as many as 1,400 voyages by the higakikaisen ships were made between Osaka and Edo.

_{Kojima, Ryouichi. The significance of reconstructed Japanese traditional wooden vessel ‘Higaki-kaisen Naniwa-maru’" 日本船舶海洋工学会講演会論文集 22 (2016): 31-36.}

Of course, this is only one route, so the total number of voyages were likely much higher.

Based on clarification from the OP, the figure of "90 incidents" came from a 1962 work by Professor Arakawa Hideotshi which, according to a bookstore listing, covered cases of adrift ships spanning ancient, medieval, and early modern Japan. It is unlikely that the given number is restricted to only sengokubune from the Tokugawa period.

It should also be noted that the sengokubune were relatively small vessels operated by only 15 people each.

Even if all "90 episodes listed by Hidetoshi" were sengokubune ships, that is a death toll of perhaps at most 1,350 (in practice, many of them would have survived on ships that were afloat, but rudderless). In 1703 alone a single storm in the English Channel killed over 1,500 sailors. So in comparative terms, judging by the currently presented evidence at least, Tokugawa shipping does not seem unusually deadly.

In fact, the "problem" of ships being blown adrift and rudderless only really manifested later into the Edo period. These ships didn't just carry tribute rice for the Shogunate, but in reality were necessary supply the whole of the eponymous metropolis. Thus, as demand at what would become Tokyo strengthened:

In other words, the growth of the shogunate capital necessitated an accompany system of mass logistics. This economic demand made it financially profitable to risk the voyage in less than ideal conditions year round.

In fact, the "problem" of ships being blown adrift and rudderless only really manifested later into the Edo period. These ships didn't just carry tribute rice for the Edo Shogunate, but in reality were necessary for supplying the whole of their eponymous metropolis. Thus, as demand at what would become Tokyo strengthened:

In other words, it was only a problem because lucrative business opportunities financially profitable to risk the voyage under less than ideal conditions year round.