For those requests excess the limit and get the response: 429 too many requests, will those requests still charge me? In this question,t he throttling limit is the limit from the API gateway itself, no other limit.
It depends.
If you reached the limit for your usage plan and the API Gateway throttles you, there would be no additional costs.
Update:
You may be billed for the requests that hit your API Gateway, even if they exceed your usage policy or throttle limits. (according to some people)
When this question was answered, the documentation explicitly stated that:
Usage plan-throttled requests are not charged when rate limits or quota exceed the preconfigured limits.
See archive.
Although, this kind of throttling may not be as accurate as you would expect, see this question: AWS API Gateway Throttling not working as expected.
If your backend integration throws a 429 (for example, you reached some kind of Lambda limit), than your request will be charged on the API Gateway.