Is there a way to export an animation as a folder of numbered files?

Do you want to export each frame as a different png file? You can use File > Save As and select a filename like image000.png (and the whole sequence will be generated, image000.png, image001.png, etc.). Also you can try the CLI:

aseprite.exe -b sprite1.aseprite --save-as folder1/image000.png
aseprite.exe -b sprite2.aseprite --save-as folder2/image000.png