De-duplication doesn't work that way. The system tracks duplicates at block level and if a configured cluster size of blocks is identical, the file block stream is chained through a single copy of the blocks. If a new version of the file appears, it will fail the block check and will have space allocated to it. If more copies of the new version then appear, they will be chained through the single copy of the new version.
If you delete a single instance of a de-duped file, it is handled the same way as multiple hard links to a file on a unix file system. The FAT entry (if you don't mind the archaic reference) is removed and the reference count to the data is decreased by one. No blocks are freed for overwrite if other FAT entries reference the blocks. So NO, an installer deleting one instance of a de-duped DLL will not remove the contents of the file from disk as the blocks are referenced by other files.