Just assign them yourself in each emulator. You only have to do it once for each emulator.
I'd reprogram the IPac to not use CTRL ALT & SHIFT. (or just don't use those terminals)
It causes issues with a few other emulators that can't use those keys for input..... and with most video cards, CTRL + ALT + Any Arrow key causes the screen to rotate.
You can disable windows hot keys, but for emulators that don't suport those keys, you would still need to have autohotkey or some other software post substitute keys.
NullDC is the only one I can think of off the top of my head that can't use those keys, but I'm sure there were one or two more.
I'd rather just use different keys to begin with.
You can remap MAME globally while any game is running.