All of the analog devices on my modular machine are USB and they all work fine.
Only issue you might eventually run into is if you have several USB devices plugged in and switch to analog mame or noname mame for multiplayer analog devices. In this case, it becomes important which device is in which port since the first one will be player 1 by default, second player 2 and so on.
Since my panels are modular (for example) if I have a bunch of USB analog devices plugged in and then try to play a 2 player lightgun game (which are also USB treated as mice) it may pus my lightguns out to player 2, 3 or 4 which can be a pain. In this case I just unplug the ones I'm not using and all is well again.
Doc-