One challenge with having the cubes grow on trees is that the player could pick a cube off a tree, carry the cube to some distance location and use that cube to open the door, then come back to the tree, pick the same cube again, and have the cube that’s being used to open the door be destroyed inadvertently.
This problem did exist when I had the cube dispensers, and it also exists in Portal 2 (which is where I got the idea for the cube dispensers from). In the case of Portal 2, the game doesn’t let you sneak boxes out of designated areas. Most puzzle areas have that field at the door which desroys any object that the player is going, so it prevents you from carrying boxes out. Also, even in cases where you should be able to sneak a box out, Portal 2 will reset the area with load scenes. Basically, Portal 2 is a pretty linear experience and doesn’t let the player break the game.
Here’s what a cube dispenser looked like in an earlier build of the game:

By pressing the button, a number of cubes (in this case 2) would be dropped down. If you re-press the button, the cubes would get destroyed, and the same number of cubes would get dropped down again.
With the cube dispenser, I think players are less likely to “reset” the cubes, since it requires pressing down on a button, and the cubes are inside the dispenser. With the tree, it’s more immediate, as you see the cube right there, available to pick.
Ryan Cousins and Alan Hazelden gave me some good suggestions with have the cube be a desaturated color if it has already been picked, or to show a “husk”. I basically combined their suggestions and had cubes that have already been picked once (meaning that it exists out there somewhere), be translucent and lighter in color. I think it does a good job of showing that the cube is not a “legit” one, or at least warning the player a bit (pick at your own caution).

Fruit Picking from Tall Trees
A really cool unexpected new gameplay that arose with having cubes grow on trees is that picking the cube becomes a bit of a puzzle, if the fruitcube is up high on a tree:

This is what it looks like to climb up the tree and pick a high fruitcube:

What’s really cool is that it becomes a bit of a platforming challenge, which I didn’t think I could do in my game with the lack of death, and being able to change gravity more or less at will. This is actually pretty fun, and offers a change in the pacing of the game, as well as presents more of a navigational puzzle than a logic puzzle.
Finally, it also just feels really fun. When you finally pick the fruitcube, and drop it down to the ground, so you can go pick another fruitcube, it really feels like you’re picking fruit!
Of course, the challenge here would be to make the platforming fun, but not tedious. I really dislike platforming in first-person myself, so definitely would not want to frustrate players on challenges that are purely execution-based.
Anyway, I’m really excited about this new gameplay aspect, and am looking forward to integrating it into the game in different areas. Pretty cool that I’m still discovering new things about the game!