It definitely is an oversight by the case manufacturers. I don't know if Apple relocated the headphone jack on the bottom out of necessity or as a design feature but if possible they really should have left it on top.
I've ordered a leather pouch case from Vaja and currently use a cheap Belkin pouch made of leather look artificial material. The Belkin doesn't accommodate the headphone jack and I'm not sure if the Vaja will either.
That said as I usually use a Bluetooth adapter it's not as big of an issue for me. Even if there was a hole at the bottom I'm not sure how practical it would be.
I emailed Beyzacases about it and they replied. Said they went with the designs they showed as they were "classic" but they are going to be releasing some new ones in the future. I personally believe they (like other manufacturers) just released a taller version of their existing designs so they had something on the market at launch. I'm going to hold off and see what Beyzacases comes up with next.
I'm sure Apple's relocation has to do with getting the "guts" of the phone in the best, most efficient layout and that meant moving the headphone jack.