I am using a Line 6 HX Stomp (USB) as input device and my Presonus Quantum 2 (Thunderbolt) as output device in Logic. I have recently experienced some very bad latency issues, too. When monitoring my input signal through guitar amp plugins I suddenly get a really bad latency up to approx. 500 ms. Sometimes it‘s not there, then suddenly it appears out of nowhere. Sometimes it helps to reload the project, sometimes not. However, it does not appear when I only use the Quantum.
This problem has only recently arisen. I have been using the HX Stomp for several months and never had any problems before. And there haven‘t been any driver updates for the HX Stomp or updates for the guitar sim plugins, which could have caused the issue. I suspect that the most recently released macOS update caused a problem with USB audio.