That is only an informative message on the relevance options panel, don't worry about that. It says, that in case you are using the index table engine, then don't forget to adjust the values on the correct panel. I just looked at it, and it works correctly, the index table is in use.
The overall plugin performance is determined by many factors – mainly the server speed and the overall wordpress performance, which can be affected hugely by the plugins count and quality. I usually recommend to use 15 plugins at maximum, but of course the number greatly depends on their qualities and performance impacts.
I recommend checking the Performance tuning chapter in the documentation, especially points 1. and 2. as those can impact the search performance greatly relatively to the server performance. (especially if you are running a shared hosting package)
If you like my products, don't forget to rate them on codecanyon :)