Will traveling to Japan during my stay in Thailand on a visa waiver affect my re-entry?

you won't have a problem. Just in case you get asked, be ready to show US Dollars equivalent of 20,000 THB in cash, a ticket out of Thailand within the 60 days you will get stamped in, and a few booked first nights after entry. You stamp history within a 1-year period will be a total of 80+60 = 140 days, which is below the maximum of 157 days on visa exempt short stays, never extended. However you might be frowned upon on your return from Japan, doing another visa-exempt entry. Because by then you have had a stay of 80+30 = 110, and another 60 days will carry you to 170 days within a one-year period. That's when you must be able to show the three proofs, again. Good Luck!

If your record is exculdes border bounces and extensions, and with regular tourist look about them you will be fine.