JPY not having any minor units is arguably not a “third party quirk” but just how the currency works. The same goes for various three decimal digit currencies.
I mean yeah, but it does make things more complicated. Currencies change to 0-decimal, but some systems still expect 2-decimal representation for backcompat reasons (like ISK and UGX in Stripe).
(To clarify some more, we’re in agreement here. My point was mainly that “just storing cents” seems like an easy solution and it might seem to be working well – until it’s not :-)