How much space does deduplication save?
According to this, you need 4096 bytes to align to actually deduplicate (or rather, save space). If I'm reading correctly, that means you would need the same 4096 bytes to occur in the blockchain somewhere at which point you would save space.

Given that each block has all sorts of essentially random data (tx id's block id's, signatures, etc), I would think 4096 bytes aligning anywhere would be highly unlikely. Most likely, you wouldn't actually save any disk space.