Yes, they're limited to 1000 rows to prevent your users overloading the system with large requests.
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No. It's a setting you can't get to on Cloud.
You might ask Atlassian support, but I don't think they let you shoot yourself in the foot in that way.
Why do you want to do this? There's probably a better way to get the information you need.
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Most of Atlassian's API's are paginated. You can just ask for the next 1000.
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