It be foolish to remove the system... especially if its already established.
In the treehouse footage of E3, there was a descriptor after Aya dug up a creature that said:
"I caught a manila clam these make amazing chowder. Yum!" "This manila clam can be used as fishing bait... I've got an idea of a DIY recipe!" whether or no this will be extended on is yet to be seen or even if entails more... (and honestly using clams as bait makes sense as i used to de-shell clams for bait...or hotdogs if i ran out...)
Nghh now I'm hungry... maybe I was a fish in a past life
In NL your character also makes a chowder comment after catching a clam so it might just be flavor text. I really hope you're right though. I wonder that we won't run out of things to craft a few months in, as more advanced furniture/accessories might need to just be purchased (to justify bells) and silver/golden tools won't break – having food recipes would add a lot more stuff to justify the crafting system.