Modifier-based shortcuts are not as good because it usually takes two hands, and maybe I want a hand free to use the mouse to scan values, operate the UI I’m testing, etc.
Also, IDEs have a ton of functions so all the simple modifier combinations are already in use. A complex two-hand combination is good for something you frequently use once while typing (e.g. “show autocomplete”). Debugging, on the other hand, is something you do relatively infrequently (hopefully!) but when you’re in that mode, it’s great to have dedicated single keys, closely clustered together.
Physical keys are much easier to use than touchscreen buttons, especially when not looking at the keyboard.