Assuming that Gosho didn't just cheat and make some random other object the murder weapon, here's one thing the culprit could've done:
A reasonably thick layer of ice could be applied to the vase opening, to seal it and keep the water inside from getting out. It would be filled almost to the top with liquid water, up until where the ice starts.
The case was stolen overnight, and ice doesn't last long at room temperature. However, the entire inside of the vase couldn't have been frozen or else it would expand and crack the vase. Hence, the entire vase was not stored in the kitchen freezer (show me a restaurant kitchen without a freezer and I'll show you a bearded woman). UNLESS...the culprit first fills the vase mostly with saltwater, which only freezes at very low temperatures, and then a little bit of freshwater at the top, which won't sink to the bottom because, as one would imagine, freshwater is lighter than salt water, which means it floats to the surface. With this trick, one could create a seal of ice to keep water in even if you turn it upside down.
I find it suspicious that the manager's brother said he went to talk to the cooks "because my sister asked me to" when it was his idea. He could've hid the vase in the freezer overnight using the aforementioned trick and then used the kitchen visit as an excuse to retrieve it for the murder. He never said anything to dismiss the possibility that he could've made himself a copy of the restaurant keys in advance and instead just kept pointing to his dislocated wrist. I don't find his wrist to be a very compelling argument; if I'm not mistaken, one can undergo surgery (and in some cases surgery is too harsh a term) to get that fixed. Had he visited a different hospital for this than the one where he got X-Rayed at, he could fool the police into falsely believing his wrist to be presently dislocated.
Keep in mind the ice seal trick has serious issues in practice. First, there's the question of him carrying/dragging the heavy vase out of the kitchen without anybody noticing. Second, there's the question of him carrying the vase to the adjacent changing room. Per the findings of the police investigation, one cannot go from the kitchen to the changing room without being easily visible to someone in the kitchen looking out.
There's a good chance that at one point Toshinori Motosu, the manager's brother was cheating on his girlfriend/fiancee with Naomura Isuzu, in a brief but passionate fling that Motosu eventually broke off. Saraie (the victim) likely obtained photographic evidence of this, which was what he meant when he threatened to "crush" Motosu. Saraie likely stored the photos on his laptop, which he could've uploaded to the internet at any time, explaining why Motosu might be desperate to get his hands on that. Isuzu likely still harbors feelings for Motosu, which is why she turned down Saraie's offer, and she figured out that her former lover is the likely culprit, and she figured out somehow that important evidence or something could be found under the counter, which is probably why she tried to divert attention away from under there when Takagi was about to take a look.