I presume these emulators have not taken to loading ROMs (or ISOs as the case may be) into RAM. If not I also assume they don't emulate load times. What type of external drive -- if you are for some reason rocking a USB2.0 drive here then the 30 megs a second it will rock (also with CPU penalty) will possibly make a difference (though it is still just about what some reckon the Wii U's speeds are).
If so then yeah look to find some lower load times than internal hard drives.