There are literally hundreds of addons and modifications available for vBulletin, all of which do vastly different things and, unfortunately, are of varying degrees of quality in their coding. As such, it isn’t feasible to ensure that the theme will work without issue with all of them.
The theme was coded in such a way as to maintain the integrity of all the hook locations that the plugin system makes use of. As such, most addons should work fine. If you are experiencing an issue with a modification, I would first direct you check out the thread at vBulletin.org where you downloaded the modification and see if you can find a resolution there. With the more popular modifications, chances are someone else has already experienced the same problem, and a solution has been posted.