The other side of it is visa overstay: it's more financially viable for working people to overstay their visa, where pure tourist have to go back at some point.
Terrorists will be flagged whatever they do, as international money transfers are already heavily scrutinized and under a working visa you still have to declare your work.
Overstaying a visa is likely a criminal offense depending on the length of the overstay, these people still have to leave the country, they're going to get caught and flagged. At a minimum they'll be prevented from re-entry but chances are there could be real punishment.
In terms of taxes, I really really doubt it, a DN is not taking a locals job, their clients & business are all out of country, their accounts and transactions are all overseas. Just figuring out what they owe and how to pay it in Japan would completely put people off using the Visa and I really doubt the Japanese government would think it worth the hassle for six months.
https://www.nta.go.jp/english/taxes/individual/12006.htm
I didn't go through all of it, but I'd expect it to be a tad less that 10% of the gross income.
If you're a US resident, I think you pay them as well on that same income ?