No, it doesn't work like that. AC has access to your program and databases just as Microsoft knows what updates you need or how your A/V programs knows when your definitions are outdated. Software reminds you when you should upgrade.
AC is simply data mining to retrieve certain information that they then share with so that your 500 transactions become 500,000 transactions and then number crunchers and analysts can deduce certain patterns from this information. So, maybe the query is to find out how many 35 to 42 year olds on xyz drug have xyz outcome. They can then predict or make assumptions based on this. Google does this, Micrososoft does this.
They are not taking your data, then marking it as not usable. They are retrieving, hopefully, unidentifiable data on those practices who did not opt out. This can be done in many different ways. But, it is almost certain this is not done in real time. It is done at certain times and likely done rather quickly.
The performance degradation would be negligible. You could use something like Wireshark to see what information is going back and forth, but given this is happening sporadically you would need very sophisticated logging and filtering.
So, the answer is no. This is not slowing your system down. If it were, then I would be seeing degradation on 6.1.2 which is super fast and fairly bug free except for one annoying thing. And, I should add, I am staying right there.
Just woke up so not a very clear answer. Sorry.