As others have said I would guess the tops as they could easily be replaced and thus the barrels reused. There are lots of references in the captains logs I have been reading to empty barrels being returned to the victualling ship.
In terms of what was on the label again I can only speculate, but there are some clues in the logs. Take for example the following entry:
It appears to me that captains were held responsible for the amount of stores they consumed as a significant portion of the logs are spent detailing what was opened when and how much it contained. From the above example we can see that here was likely some sort of reference number on the barrel (in this case N 212). I assume N refers to No or Number, but it is not clear if the N would have been included or just the number. Also it seems likely to me that there was some indication of much the barrel contained (in this case pork). The reason I suspect this is pretty much every time a food barrel was opened, he details how much was in it.
I have tonnes of examples like these I could show you if you wanted to see them.
In summary I would say if the barrel in question contained food, I would expect a label on the lid with a number (e.g. N212), the product in question (e.g. salt pork), and the amount of the product contained within.
One final note is that it only seems to be the meat that was catalogued in such detail. The logs are much more vague with regard to other commodities being consumed though they do carefully not the number and types of barrels brought on board.
As Chris said really it is up to you. The reality is that the state of a deck would have changed significantly depending on the circumstances (are they cleared for action or just sailing along). So you have essentially two choices:
Pick the exact scenario you are trying to depict and do so accurately (e.g. show the tackles laid out if the ship was ready for action or shut the ports and secure the cannons to the side of the bulwarks if just sailing along).
Do some sort of representative scenario (this is what most people are trying to do). Essentially you are depicting some of the many things that were done on the ship even though it is technically inaccurate to have them happening simultaneously. But in this case it comes down to what you want to depict and how aesthetically you want to present it (a ship model is a work of art after all).
Though with #1 there might be a technical right answer there is most definitely no right answer to number two as it depends on what YOU are trying to depict.
Thukydides's post in What’s in a barrel? was marked as the answer