I got them in a package of "mixed denomination" bills when I bought cash from my bank before leaving for Japan also. I think American banks probably got a stock of the bills years ago and have been trying to get rid of them ever since.
Although the exchange rate has changed the math, I just think of the various bills as 1k = $10.00, 2k = $20.00, 5k = $50.00 and 10k = $100.00. Back a few years ago, when the rate was close to 100 to 1, this worked pretty well. Now they are worth a little more but the "feeling" is about the same.
Some older vending machines may not accept the bills but most newer ones will. I generally try to use the 2k bills whenever I can and save some 1k and 5k bills for those times the 2k may be problematic. Carrying cash in Japan is not a problem as it might be in many US cities. I am one who prefers to avoid routine credit card use except for large purchases like hotels so always have a fair amount of cash on me.