If you're working with euros your largest denomination coin is 2€ . In Yen it's 500 yen! This is not chump change and just throwing those coins into the charity box can leave you with effectively increasing your lunch pricing by 50% if you have a "give all coins to charity" policy.
If you have the cash for it more power to you, of course.
500 yen's over £3, so I'm guessing you don't get many of those in your lunch change? The top result for "how much is lunch in Japan" [1] suggests that your 500 yen coin would just about cover the next day's lunch and is lighter (barely; 7 grams versus 8.75g) than a British one pound coin [2,3].
The coin sorting machines that you might tip a coin jar into take a decent chunk of your money for the privilege of counting it (e.g. CoinStar charge 9.9% [4]).
1: https://www.withhusbandintow.com/costs-to-eat-in-japan/
2: https://en.wikipedia.org/wiki/One_pound_(British_coin)
That works even when coins have non-trivial value.
Also, taking out $100 in 2017 is silly, at least if you spend more than $200 a week, which is most non-students here. I just get out the max that the ATM will let me have and I never regret it.
"But what if I get mugged?" This is silly. If you actually do get mugged, you want to have a big load of money on you, not $3.29. Happy muggers mean fewer dead programmers.