The only limits I've seen for Route53 are the number of hosted zones (50 by default?) and I don't see why that would be an issue. You'd only need one zone per app environment (dev/qa/prod).
>All requests – Five requests per second per AWS account. If you submit more than five requests per second, Amazon Route 53 returns an HTTP 400 error (Bad request). The response header also includes a Code element with a value of Throttling and a Message element with a value of Rate exceeded.
Though the general AWS recommendation for API limits is implementing exponential backoff + jitter.
http://docs.aws.amazon.com/general/latest/gr/api-retries.htm...
I suppose you can take it a bit further by batching requests (says up to 100 changes per request) but that would complicate distributed apps where the requests aren't coming from one coordinator.