I think windows sees it as a gamepad.
Yeah I'm wondering about set up, with two of the same boards, Not sure if Mame will be able to tell the difference between exact boards.
Gamepad: then Mame will be fine.
Windows might switch the two's numbers on reboot or after unplug/replug in special conditions. This would just switch which player each pad controls in mame. If you don't mind this sometimes happening, don't worry about it.
That's why ultimarc & GGG let you change their encoders' (USB product) IDs: with different IDs; this way windows doesn't mix them up. I'm not sure if the Cthulhu can be given different IDs, also. (If they have different IDs, the borad you plug in first will control player 3, the second player 4, assuming you remap as follows.)
As for setup, you'll need to remap maps inputs, so joystick #1 controls player 3, and joystick #2 controls player 4. The easiest is plug in (install) all boards, enable joysticks (and maybe mice if you want) in mame, start any game, tab, select "inputs (general)", select to player 3, and remap them to use joystick #1 (stick and buttons). Repeat for player 4. Now you have to unmap those joysticks from player 1 & 2, since the the default is for kthe keyboard or joystick 1 to control player 1, ditto player 2. Go to player 1, and map the correct stick and buttons on the main encoder.
I suggest backing up the resulting file in cfg folder, default.cfg, so you don't have to remap again (say, when you upgrade mame, or someone acciedentally messes up the mapping).