I bought a 2020 Australian Baby Proof set for the normal price of around $120. I only wanted the unique coloured 50 cent that was in it for my collection. Once I broke the set up to get that coin I sold the remaining individual coins for more than I bought the set for.
In effect I got the coloured 50c for free. They normally sell for $100 or more by themselves. Here it is.
My general rule of thumb is to keep it in original packaging and that this does tend to bring more value when it comes time to resale. You did however mention that the packaging has been severely damaged by water so in this case I would say you will be just as well off removing them from the packaging as long as you take care in doing so and store them properly. If it’s just minor damage though or cosmetic even I would say keep it in the packaging as long as there is t a chance of it degrading and in turn damaging the coins. Also as a final option it’s amazing the things you can find on eBay and you might even consider purchasing a replacement case from someone that removed theirs. I see it pretty frequently especially with coins that people sent off to be graded selling the empty packaging for next to nothing on eBay.
I hope my late night rambling helps answer your questions.
Matt