Solution:

The murderer is Marcus.

The notes hinted towards the name of Marcus. How?
Just take the first letter from Compound, Art Room, Restroom, Underwater Room, Study Room and Movie Room and you will get:

C, A, R, U, S and M.

Rearranging these words leads to the name Marcus who is the murderer.

Solution:

See the figure for the answer. Wasn't it a bit tricky?

Solution:

The matchsticks that are marked with red are to be removed and the final figure will have just two squares. You can remove either pair from the possible four ways.

Solution:

The Bangladeshi seaman is the thief. This is because the Japanese flag cannot be identified as upside down as it is the same both ways. Thus he is just trying to escape the situation.

Solution:

2 people

Say 2 helpers are Helper1 & Helper2

Helper1 food Helper2 food McDuck's Food
End of Day 1 : 1 4 4
Now 'A' will head back

End of Day 2 : N/A 2 4
Now 'B' will head back

Now Mr. McDuck have 4 day food :-)

Solution:

You will ask, I have a number in my mind that i.e. either 2 or 3. Is the number that I have in my mind smaller or equal to the number that you are thinking of?

If Alan replies with no, he is thinking of the number 1.
If Alan replies with yes, he is thinking of the number 3.
If Alan replies with don't know, he is thinking of the number 2.

Solution:

We now have a square of 3x3 size, 2 squares of 2x2 size and 5 squares of 1x1 size.

Solution:

7, 4, 6, 5, 8

Solution:

When you were inside the shed, the murderer replaced the lock with his own one that was identical to your original lock. When you locked the store room, you did not require a key and there was nothing abnormal for you. When you left, the murderer opened the lock with his key, planted the dead body inside and replaced the lock again putting the original lock in the place. He then closed it without any problem.

Solution:

20
Just count the nines in the numbers: 6, 16, 26, 36, 46, 56, 76, 86, 96, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69.
Note: 66 contains TWO nines

Solution:

Kid1, he was left with one rock.