In ATX, no, we'll none that I know of have openings for vertical gpu. There are a couple from Lian-Li, Phanteks and a few others which have extra modular mounts for larger cards, offsetting them closer to the mobo, but that also can be problematic and require the use of a riser with a 90° connection for the mobo. And even then, a 3x card is looking at 1" to 1/2" or sometimes less.
I ran a gtx970 with a 280mm AIO for years in a FD Define R5, with ssds. So I fully get that whole 'there's nothing but space in there' empty box looking case thing. Which btw does complicate airflow since components are far enough away to require high sp fans just to get air to the components.
mITX, even many mATX cases are generally far more suited for airflow than an ATX midtower, even with less fans as the volume of air moved is generally faster. With just 2x 120mm fans a SFF can replace the entire volume of air in less than 30 seconds. With 5x 120mm fans, an ATX mid takes over 2 minutes.