What is the difference between "x IS NULL" and "NOT (x IS NOT NULL)"?
Use EXPLAIN to see the difference, if there is any.
I think the query rewriter will optimize this, but I didn't check the source code for this example.
Edit: I was wrong, this is not optimized at all. Where ("users"."deleted_at" IS NULL) can use an index, the (NOT ("users"."deleted_at" IS NOT NULL)) condition results in a sequential disk scan.