I volunteer with a small US-based non-profit publisher [0], and this all matches my experience. We publish black-and-white technical journals that are worth almost nothing, and our European subscribers have occasionally been charged 20€ per copy by their customs authorities [1].
We're now prepaying the duties, which seems to have solved that problem, but a few months ago our printer informed us that we will now have to pay this additional €3 fee per copy, plus some undisclosed additional markup charged by the shipping intermediary. But at least they'll handle everything for us without any paperwork, so this is just expensive rather than a bureaucratic nightmare.
But unfortunately this fee seems unavoidable for us—we only mail ~300 copies to Europe per issue, so having multiple printing locations is infeasible; I've checked with a few other printers and they all quoted me double what our current printer charges, so it would be way too expensive to print everything in Europe; and timeliness is important for a periodical, so people can't just order in bulk. So it seems like we'll probably just have to raise our subscription rates again to cover these fees.