The fact that clicking on the #1,0 will join 0 also
It doesn't.
It ALWAYS joins the first channel listed (based on the comma as delimiter) just as I said, and as you quoted,
If you click on #1,0 you will join #1, if you click on #1,000 you will join #1 - no matter where on the string you click.

NEVER will mIRC join "000" from a double click, unless you have scripted #channel hotlinks, in which case it is not mIRCs fault.