It's difficult to anser your question, as it's asking about two different things at the same time and you've not provided any code that shows HOW you are getting the Issues; using which Jira API endpoints, what parameter values used and which Authentication method etc.

Jira's rate limits are calculated as a 'cost', based on activity over time for a particular access method based on the authentication type, so its a quantitive measure, which has nothing to do with getting Issues in any particular hierarchy order or depth.

As long as you get all the Issues you want at a reasonable rate, over a reasonable time, you'll not hit the rate limit. Just watch the API responses for the rate limit approach warnings and then 'back off' your requests to stay within the limit.