Experience suggests that if you loot for x hours with y men, you will burn more food if the warehouses have 5000 bushels than if they have 200. Therefore, to maximize food burnt ratio by men by hours spent, it is preferable to attack them when the warehouses are the most filled.
Also, if you can loot enough to provoke starvation, then doing so earlier can extend the starvation period as well.
My observations may have been misleading, however.
Actually, on average, the warehouses are most filled during winter. For most realms, of course, the absolute most food in the warehouses would (generally) be either the last day of autumn or the first day of winter (depending on how the game calculates things). However, barring changes in food supply other than seasonal changes (obviously never the case), amount of food in the warehouses at the start of autumn is:
S
and at the end is:
S + 2H - C
where S equals initial stores, H equals normal daily harvest, and C equals daily consumption. In winter it is at the beginning:
S + 2H - C
and at the end:
S + 9/4H - 2C
There are more elegant formulas to find the average at any time, but I forget enough statistics that I'll leave that for another time or someone else. But basically, for realms that have more or less equal production and consumption (or higher production than consumption), you end winter with more food than you began autumn.
In short: storehouses are most filled at the end of autumn and beginning of winter with a slight skew towards winter because they don't empty as fast as they fill.