This definitely still happens, but I think implicit in your post and this thread in general is the unstated statement "...and this is a horrible state of affairs that shouldn't persist for even one more day!".
Ultimately it's the credit card companies that regulate this playing field, and up to a certain point they're happy to make a large trade-off between security & convenience, because they can work the security issues into their processing fees.
Credit card companies aren't dumb, of course they know that small Mom & Pop hotels are going to have horrible security practices when it comes to credit cards. They also know that any security issues are going to be contained to the customers of that establishment.
This is why PCI puts a huge amount compliance burden on companies such as payment processors and travel agencies that process a lot of credit cards, but by-and-large ignore small players.
The hotelier you described and his method of ad-hoc charging credit cards with a 10% fee at some unrelated business is surely in violation of some PCI rule(s), but that's going to be a matter between his customers and his bank, not all customers of the travel agency and Visa/MasterCard.