The reason you never see trees with more than 8 or 9 food is because when they drop to 7 food, villagers will not harvest from them. It takes very very little time for villagers to strip a tree; in all the time I've been playing, I've never once been sitting there to see a tree refresh itself, and I've never once loaded the game in between a tree refreshing itself, and the villagers stripping it bare again. I would look to your population as the culprit; the honeycomb may look like it can sustain a few villagers indefinitely, but that's an illusion caused by the 500 food it comes with. The regeneration of the honeycomb cannot indefinitely support a single villager. The orchard, likewise, can sustain many villagers in the short term, but only around a dozen villagers long enough to get another source of food, and only four villagers indefinitely. (More if you don't mind them going hungry now and again.)

The trees regenerate 111 food every 3 hours, if I remember correctly. Additionally, each tree arrives with 1000 food when it matures. This is the reason for the illusion that the trees can support many more villagers than they actually can support alone. I wouldn't expect it to support more than 10-12 in the time it takes you to get the tech needed for another food source.

Remember, when it rains, it's a mushroom fiesta! Get gathering! You can sustain ten people on mushrooms alone, if you're vigilant, and if you pause the game before quitting. Pausing also has the advantage of being able to use the chief powers much more often, from the villager's point of view.

The 'guides' section has detailed solutions to the puzzles clearly marked. Since this thread isn't marked spoiler, I won't post solutions here, but the topic should be easy to find over in the guides section.

Here it is:
Virtual Villagers 3 Tips, Tricks, Hints, Spoilers
This guide is chock-full of spoilers, so beware.