As far as Im informed, you will lose nothing.
It doesnt matter whether you use a OS software/script. Its a matter of visitors on your sites. So you can practicly have a blank html page with the woopra script in :P
Although keep in mind that the current woopra version might not show the full url on where the user is. E.g if your website is mysite.com/index.php?page=3322 - it might not show page=3322 but it will however show the title of the current page the visitor is browsing.
This issue with not showing the full url has been noticing by 2 or 3 people here. But thats about a small detail I think, cuz you are going to be able to see the title of the page anyways, and this issue miight not even affect ur site.