Do they still exist? Yes, but...
For years, manual transmissions cost less than their automatic counterparts. The latter was viewed by automakers and consumers as a premium feature. And then for some cars, such as the Porsche 911, the situation morphed into manuals becoming a no-cost option. Unless specifically requested by the buyer, an automatic or dual-clutch would was standard. But times are changing. Again.
According to Cars Direct, manual transmissions are actually becoming more expensive in certain segments, specifically hatchbacks. The proof is in the numbers, as usual. Take the all-new 2019 Mazda3 hatchback, for example. It carries a base price of $21,895, but if you want one with a six-speed manual then you'll have to pony up at least $28,395 for Premium trim.
Yes, you'd be receiving other features as well aside from the manual, but you'd still be paying $6,500 more to row your own gears. Buyers could get the outgoing Mazda3 with a manual for as little as $20,240. In other words, from one model year to the next the price of a manual-equipped Mazda3 went up by $8,100.
Here's another example: the 2019 Hyundai Elantra GT can no longer be equipped with a six-speed manual in base trim for a darn reasonable $20,235. Today, you'll have to pay an additional $4,000 or so for the new N-Line model that can be had with a manual. Another casualty is the 2019 Honda Civic LX hatchback. Its six-speed manual option is gone. Honda is now forcing buyers to pay at least $23,170 for the manual-equipped Sport trim – a $2,100 increase.
As for Toyota, it discontinued the Yaris in the US for 2019 and also the least expensive manual you could get from the brand. The all-new 2019 Corolla hatchback has a fine six-speed gearbox, but its base price is $20,920 – a $4,300 increase over the Yaris.
To summarize what's happening here, automakers have determined the take rate for manuals in America continues to drop, though there are still enough willing buyers. Unfortunately for them, automakers are tying the manual with sportier and more expensive trims. Manuals are used to please enthusiast buyers, but they'll have to pay more for that enthusiasm.