If I delete my ipad kindle app, will my books remain on my kindle device? Will they remain in the ipad icloud storage?
Generally Amazon offers a cloud solution for your ebooks, so removing the purchased ebook from your app or removing the app entirely is very unlikely to cause a deletion on your cloud storage.
On my android device, I don't see any option to remove the ebook permanently -- which leads me to assume that you cannot delete it on all devices and your cloud from one device. (You probably can do a permanent deletion from the Amazon website under Manage Your Content and Devices so be careful.