Reaction backpack by Kenneth Cole has four lockable pouches. Laptop pouch is well padded. The sleeve on the sides is too short for a full size water bottle.
The end of the zippers have a hole to lock a luggage padlock on. I don't think Medeco manufacturers luggage padlocks.
Abloy manufacturers high security luggage padlocks but they are not rekeyable. Local locksmiths do not have Abloy blanks to make more keys.
I purchased these combination luggage padlocks:
I have a solution that's similar to what u/Iam-Nothere and u/Serindu suggested.
This box from Amazon seems like it's the size you're looking for (6.7 x 5.1 x 3.1). It's around $13 and I'm sure you could buy similar boxes in bulk at an even cheaper price.
It turns out you can remove the latch and replace it (almost directly) with this hasp that has a latch lock.
In my initial test, I replaced the top piece directly and had to move the bottom piece up slightly. Since the wood is soft (it's pine), you can just reposition and re-screw the hasp manually (without needing power tools).
The hasp is big enough to fit most standard combination locks. For example, this 3 digit lock and this 4 digit lock both fit the hasp (but for the box I linked they're a bit too tall). A smaller padlock like this fit the box and hasp perfectly.