Hi,
I don’t think you should do that, as I am not entirely sure if that is the cause.
I did a few more experiments, and whenever an exclusion is made for a separate taxonomy (not category), then simply everything is excluded. I am not sure if this is an exception of some sort, or perhaps a yet unkonw bug.
Anyways, I have constructed a custom code, that may get around it. This script will turn on/off the empty taxonomy argument, depending if there is anything selected within the filter. Basically, by default it will allow searching everything (except the exclusions of course), then when any checkbox is checked, it won’t allow the missing terms option. I am almost certain that this should get around the issue.
Add this custom code to the functions.php in your theme/child theme directory (copy from line 3 only!). Before editing, please make sure to have a full site back-up just in case!