If calibre would see them as duplicates, yes.
SmartEject does three different searches:
- Dups: From the Library, search ondevice:"("
- Deleted: From each device location (Main, Card A & Card B), search inlibrary:False
- Added: From the Library, search not ondevice:"~[a-z]"
My experience is that the dup search will find the same book in different places on my Android smart phone. I assume your Android tablet would work the same.
However, you might cause yourself problems with some reader apps if you just delete the files. Aldiko comes to mind as one that manages it's own library.