Why are deleted emails no longer stored in Smart Mailboxes?

A Smart Mailbox doesn’t store messages. It is just a search that displays messages that match its criteria. When you delete the message, it doesn’t exist anymore so the Smart Mailbox cannot find it to display.

If you want to file away the messages, create a real mailbox and move the messages into that mailbox after processing them.

Do you mean emails that are in the trash or actually deleted? The latter would not be possible since a smart mailbox searches for items that matches criteria. I haven’t looked, but perhaps they no longer search the trash.

The only way you could’ve seen them in a smart mailbox before is if they weren’t actually deleted. If you were just talking about if you move them to the Trash, then then there is a setting in the Smart Mailbox criteria to view items in the Trash. You can edit the smart mailbox and check that box, but if you actually deleted the email it won’t show now nor did it ever show in the past in a Smart Mailbox

I got a chance to view my Smart Mailboxes and there is a checkbox to include items from the Trash.

I don't know if that is a change. Rules have always had that option.