As you say, this is almost certainly a violation of the Statute of Wizarding Secrecy. Then again, it's probably a low-risk violation, because...
As far as an outside observer can tell, Jacob has a box full of silver shards
Newt mentions earlier in the film that Occamy eggs are pure silver:
Newt: See, their shells are made of silver so they're incredibly valuable.
Fantastic Beasts and Where to Find Them: The Original Screenplay
So, as far as Jacob's (possibly) Obliviated mind knows, some anonymous stranger gave him a box filled with shards of pure silver, that happen to be in the shape of eggshells, and a note speaking complete nonsense; there's very little to connect Newt's gift to the existence of wizards and magic.
Likewise, there's no reason Jacob should struggle to use the shells in muggle society:
- Any muggle who sees the note would assume that it was written by a crazy person
- Anyone who sees the eggshells (regardless of whether they saw the note) would just see a bunch of fragments of silver, possibly originating from some egg-shaped decoration
Bearing in mind the marvelous human tendency for self-delusion, there's little-to-no reason to connect the box and the note to the existence of magic and wizarding society; you might take it as evidence if you were already inclined to believe that, but it's unlikely to, in and of itself, lead someone to that conclusion.