Keys that are used for hotstrings don't get passed to your slaves by default, surely? They get translated into a string which the slaves use to generate a new keystroke and not passed as a "raw" key. All you should need to do is add your hotstring keys to the whitelist and forget about them.

I'm a user of a blacklist (I blacklist all the alphanumerics, punctuation, smiley brackets + slash and enter keys in both open and shifted modes) this still allows me to use ctrl/alt anything while never having to mute just to talk. For logging in or multichar emotes I just set a DNP override to "scroll lock".

I'm new to Keyclone, so it's possible I've either mis-understood or made an error.