1. There is generally no reason to expect a decrease in performance, in my opinion. I interpret that link as explaining that using the accelerator simulation modes may not accelerate Stateflow charts and MATLAB Function Block substantially because those blocks always generate code for simulation. Though, that is not always true.
One consideration I've seen is that model update can be a bit slower when the model contains many MATLAB Function Blocks. The time to write code to disk and compile it can introduce a little latency.
Note that in R2015a a new feature was added that uses just-in-time (JIT) compilation to remove the need for this intermediate code generation for many MATLAB Function Blocks. Search for "JIT" in the release notes for more information.
