1.
No, that would be a symbolic link. Having two hardlinks literally means having the same file twice at different paths. Modifying /path/to/A will modify /path/to/B and the physical data on disk will only be freed once all hardlinks have been deleted.
Keep in mind that when you say "file" you actually mean "hardlink". It's the same thing. Deleting the file / hardlink in the original location does not affect the file / hardlink in the new location. Physical data on disk will be freed once all hardlinks to it are deleted.
2.
There is a series format and a anime format. Separating tv show from anime episodes is not always possible because anime are inherently tv shows. If a file is recognized as tv show, then it'll be different to separate "anime" from "tv shows" because there is no "this is an anime" flag in TheTVDB. The only correct way to do this is forcing anime mode via ut_label. Please refer to the amc manual for details.
@see
viewtopic.php?f=4&t=215
@see
viewtopic.php?f=4&t=1508