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They are allowed in the ePUB specification. In fact, the images folder is not dictated by the specifications either. It is good practice since it keeps things clear and separated. However, since having a few hundred images in an ePUB is rare, usually one folder is enough. Sigil does not support multiple folders in an ePUB. In fact, if you have subfolders in your images folder, upon opening in Sigil they will be merged in one folder and all the references to them will be adjusted so everything will keep on working.
If you create additional folders and move images to them (like you did with eCanCrusher), everything should be working fine, as long as you also adapt the references to the image. After all, the image is at another location so the links must be updated to reflect that change.
Now, I believe that the editor in Calibre does support multiple folders. I am not sure though, as I do not use the Calibre editor for several reasons myself. Call it personal preference. From what I heard, it is also a good editor.
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