Hi,
Please post an exact code sample that I could test as I am not able to reproduce this. I tried the following on the default demo in the download package:
<li><a href="#">Introduction to SmartMenus jQuery<a href="#" style="display:none;">hidden link</a></a></li>
The item does not disappear if I click it (just its parent sub menu is deactivated).
Normally the script shouldn’t copy any attributes the way you describe. I guess some other script on your page is doing that.
Thanks!