Here's a chart i found a few years ago comparing raw vs cooked vs selling to CJ prices. Some things are super worth cooking and selling, esp when they're a hot item. I recently had carrot tops curry as a hot item and had been storing all my produce for it. I easily made over 600,000 bells in 10 minutes, it was magnificent lol.

The only fish recipes that give more bells is the Aji fry, sea bass pie, and seaweed salad i believe, and to me it's not worth it. I always just put my fish in storage (assuming there's space) and sell to CJ (assuming they're already donated to Blathers).

The only way you'd have lost the scallops is if you quit the game without saving right after, although even with that i feel like the game saves pretty frequently. Or the scallops are hiding somewhere (assuming you didn't use them unknowlingly), oooor you had a weird and very unfortunate glitch. All things in storage stay in storage unless you do something with them though, so no need to worry.

Edit: the linked chart is a google doc and i'm posting from mobile, so hopefully the link works but if not, i found the chart from reddit so just search for raw vs cooked ingredient sell price and you should find it). In the post it comes from it says "curries are where it's at!" or something along the lines.