>I can't seem to page through the results (they return a maximum of 200)
Paging is done through the 'offset' parameter
>Filtering via Folder only returns the immediate child results, not any child emails that are 1+ steps removed (emails that are nested within a program or other folder aren't included).
Correct, the folder filter only looks at the immediate parent of an email asset. Most use cases require retrieving the entirety of the set of emails though, and cross-referencing them. If you need to search through a folder tree, then Get Folder Contents is better suited to your needs: http://developers.marketo.com/rest-api/endpoint-reference/asset-endpoint-reference/#!/Folders/getFolderContentUsingGET