The only filtering available for the layer drop-down is to hide 'locked' layers. There isn't an option to hide invisible ones.
So, you could change the settings for your layer combos so that all invisible layers are locked to achieve what you're asking for. But, this does then make it hard to quickly move something to an invisible layer (e.g., hidden cutting object layer, recycle bin layer, etc)... so you might want to leave a few key hidden layers unlocked.
Hiding locked layers from the drop-down is a setting in the Work Environment...see attached.
