The first problem with your example is that NetApp deduplication occurs at the block level, not the file level. The second problem is, given the number of systems in the field utilizing it - if your example were accurate there would be literally THOUSANDS of people up in arms.

Furthermore, their deduplication is post-process, so even if dedup were to somehow modify atime, which it doesn't, you wouldn't have seen the access time change for at best 24 hours after the file was modified.

Troll on.