There are two parts to this: First is the game. Second is the story. And there is absolutely no reason whatsoever to ever bother putting the two together if you're going to worry about the bag of rats.
The Long Rest, Short Rest, and spell slots are purely GAME terms and game mechanics. When you "game the system" you are literally doing that-- you are
playing the game. You aren't concerned about story, you aren't concerned about narrative, you aren't concerned about what is happening "out in the world". All you are concerned about is using the rules that allow you to have a game rule (spell) active, while regaining a game rule (spell slot) right after, via the use of a game rule (Short Rest).
If you are going to do that... or if you as a DM is going to allow a player to do that... then just do it. The player has a 24 hour spell going "for free" and still has the applicable spell slot. Just own it. Own the fact that the PC has this ability. Be happy about it. Enjoy it. You are using game rules to give your character game power. If you're good with that... then be good with it.
But what you
shouldn't do is waste your or anyone else's time in trying to come up with some wishy-washy explanation in the game world why this is happening. Because narratively the whole thing is stupid. "Oh, I just woke up from an overnight sleep and now I'm going to use my magical power on this fuzzy animal before killing it... and then I'm going to lay back down and read a book for an hour so I can get my magic back. And then I'll get back up and continue on with my day."
Why are you bothering trying to justify that? We all know that narratively it's dumb and is a big lame story hoop you are spouting just to make it seem like you're still "in the world". You are trying to exploit the game rules "because the game rules allow you to"... and then trying to tie the story up into a pretzel so you can feel better about it.
Nobody cares. If you want a 24 hour Hex and all of your spell slots for the day... then just take 'em. Do it. Own your desire and stop wasting our time trying to make us not feel like you're "cheating" or "gaming the system".
You know it's lame, we know it's lame, and it's all because the rules were not written so goddamn airtight to
stop people from being lame. So be lame. Accept it. Embrace it. Enjoy your spell and your spell slot and have a great day out there adventuring. All while saving us the need to watch you "in-story" walking around with a squeaking bag of rodents.
Hell, I'm surprised WotC didn't bother just making a rat one of the material components for the spell at this point.