In this case, I really doubt this extension would hurt him - how the extension works is just like uBlock uses lists to hide things, AdNauseam uses the same lists to explicitly click on those items. His own ads wouldn't match any of the rules in those lists and unless they are extremely obnoxious nobody would bother adding his ads in there.

If he does get on one of those lists it's quite easy to change the markup of the page (class names, etc) to stop the rules from matching. If you're doing the right thing by hosting your own ads you fully control the markup and layout and it becomes extremely easy to protect yourself from this.